rs10216243

Variant names:

• chr7-104873177-C-A
• rs10216243
• NM_199000.3:c.683-33010C>A

Your query was ambiguous. Multiple possible variants found:

• chr7-104873177-C-A
• chr7-104873177-C-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_199000.3(LHFPL3):​c.683-33010C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0876 in 152,238 control chromosomes in the GnomAD database, including 1,253 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.088 (1253 hom., cov: 32)
• Consequence: LHFPL3 NM_199000.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130
• Publications: 1 publications found

Genes affected

LHFPL3 (HGNC:6589): (LHFPL tetraspan subfamily member 3) This gene is a member of the lipoma HMGIC fusion partner (LHFP) gene family, which is a subset of the superfamily of tetraspan transmembrane protein encoding genes. Mutations in one LHFP-like gene result in deafness in humans and mice, and a second LHFP-like gene is fused to a high-mobility group gene in a translocation-associated lipoma. A partial gene fragment named LHFPL4 corresponds to a portion of the first exon of this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LHFPL3	NM_199000.3	c.683-33010C>A		intron_variant	Intron 2 of 2	ENST00000424859.7	NP_945351.1
LHFPL3	NM_001386065.1	c.*31+27748C>A		intron_variant	Intron 3 of 3		NP_001372994.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LHFPL3	ENST00000424859.7	c.683-33010C>A		intron_variant	Intron 2 of 2	1	NM_199000.3	ENSP00000393128.2
LHFPL3	ENST00000401970.3	c.*31+27748C>A		intron_variant	Intron 3 of 3	1		ENSP00000385374.3
LHFPL3	ENST00000683240.1	n.*290-33010C>A		intron_variant	Intron 3 of 3			ENSP00000508253.1
LHFPL3	ENST00000684090.1	n.261-33010C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0875 AC: 13312 AN: 152120 Hom.: 1252 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.0138

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.0677

Gnomad FIN AF: 0.0414

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0206

Gnomad OTH AF: 0.0755

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0876 AC: 13331 AN: 152238 Hom.: 1253 Cov.: 32 AF XY: 0.0915 AC XY: 6809 AN XY: 74420

African (AFR) AF: 0.173 AC: 7174 AN: 41532

American (AMR) AF: 0.100 AC: 1531 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0138 AC: 48 AN: 3472

East Asian (EAS) AF: 0.431 AC: 2232 AN: 5176

South Asian (SAS) AF: 0.0673 AC: 325 AN: 4826

European-Finnish (FIN) AF: 0.0414 AC: 439 AN: 10596

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0206 AC: 1403 AN: 68024

Other (OTH) AF: 0.0794 AC: 168 AN: 2116

Alfa AF: 0.0406 Hom.: 874

Bravo AF: 0.0965

Asia WGS AF: 0.260 AC: 899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.15
DANN	Benign	0.68
PhyloP100		-0.013
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: rs10216243; hg19: chr7-104513624;