rs6788865

Variant names:

• chr3-185508608-A-G
• rs6788865
• NM_139248.3:c.*182T>C

Your query was ambiguous. Multiple possible variants found:

• chr3-185508608-A-G
• chr3-185508608-A-T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_139248.3(LIPH):​c.*182T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 613,392 control chromosomes in the GnomAD database, including 53,832 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.42 (13639 hom., cov: 34)
  • Exomes 𝑓: 0.41 (40193 hom.)
• Consequence: LIPH NM_139248.3 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.208
• Publications: 8 publications found

Genes affected

LIPH (HGNC:18483): (lipase H) This gene encodes a membrane-bound member of the mammalian triglyceride lipase family. It catalyzes the production of 2-acyl lysophosphatidic acid (LPA), which is a lipid mediator with diverse biological properties that include platelet aggregation, smooth muscle contraction, and stimulation of cell proliferation and motility. [provided by RefSeq, Jul 2008]

LIPH Gene-Disease associations (from GenCC):

• hypotrichosis 7

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
• hypotrichosis simplex

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• isolated familial wooly hair disorder

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

TMEM41A-DT (HGNC:58335):

ENSG00000309120 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 3-185508608-A-G is Benign according to our data. Variant chr3-185508608-A-G is described in ClinVar as Benign. ClinVar VariationId is 1179532.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_139248.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIPH	NM_139248.3	MANE Select	c.*182T>C		3_prime_UTR	Exon 10 of 10	NP_640341.1	Q8WWY8
	LIPH	NM_001438651.1		c.*182T>C		3_prime_UTR	Exon 9 of 9	NP_001425580.1
	LIPH	NM_001438029.1		c.*182T>C		3_prime_UTR	Exon 9 of 9	NP_001424958.1	A2IBA6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIPH	ENST00000296252.9	TSL:1 MANE Select	c.*182T>C		3_prime_UTR	Exon 10 of 10	ENSP00000296252.4	Q8WWY8
	LIPH	ENST00000424591.6	TSL:1	c.*182T>C		3_prime_UTR	Exon 9 of 9	ENSP00000396384.2	A2IBA6
	LIPH	ENST00000953488.1		c.*182T>C		3_prime_UTR	Exon 10 of 10	ENSP00000623547.1

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63960 AN: 152036 Hom.: 13627 Cov.: 34

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.430

GnomAD4 exome AF: 0.411 AC: 189381 AN: 461238 Hom.: 40193 Cov.: 4 AF XY: 0.403 AC XY: 99605 AN XY: 247018

African (AFR) AF: 0.409 AC: 5171 AN: 12636

American (AMR) AF: 0.384 AC: 8827 AN: 22990

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 6345 AN: 14760

East Asian (EAS) AF: 0.307 AC: 9178 AN: 29858

South Asian (SAS) AF: 0.288 AC: 13914 AN: 48358

European-Finnish (FIN) AF: 0.408 AC: 12262 AN: 30066

Middle Eastern (MID) AF: 0.436 AC: 927 AN: 2126

European-Non Finnish (NFE) AF: 0.444 AC: 121829 AN: 274432

Other (OTH) AF: 0.420 AC: 10928 AN: 26012

GnomAD4 genome AF: 0.421 AC: 63997 AN: 152154 Hom.: 13639 Cov.: 34 AF XY: 0.417 AC XY: 30997 AN XY: 74390

African (AFR) AF: 0.412 AC: 17090 AN: 41512

American (AMR) AF: 0.413 AC: 6309 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1573 AN: 3470

East Asian (EAS) AF: 0.300 AC: 1550 AN: 5174

South Asian (SAS) AF: 0.260 AC: 1256 AN: 4828

European-Finnish (FIN) AF: 0.414 AC: 4377 AN: 10580

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30275 AN: 67978

Other (OTH) AF: 0.432 AC: 914 AN: 2114

Alfa AF: 0.434 Hom.: 18527

Bravo AF: 0.423

Asia WGS AF: 0.314 AC: 1092 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.3
DANN	Benign	0.59
PhyloP100		0.21
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6788865; hg19: chr3-185226396; COSMIC: COSV107357804;