NM_001321350.2:c.-681C>T

Variant names:

• chr17-32007642-C-T
• rs544987121
• NM_001321350.2:c.-681C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The NM_001321350.2(LRRC37B):​c.-681C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00162 in 151,452 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.0016 (2 hom., cov: 32)
• Consequence: LRRC37B NM_001321350.2 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.733
• Publications: 0 publications found

Genes affected

LRRC37B (HGNC:29070): (leucine rich repeat containing 37B) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

LOC124903972 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BP6: Variant 17-32007642-C-T is Benign according to our data. Variant chr17-32007642-C-T is described in ClinVar as Benign. ClinVar VariationId is 2647655.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 2 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001321350.2. 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
	LRRC37B	NM_001321350.2	MANE Select	c.-681C>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 15	NP_001308279.1	F5H5K1
	LRRC37B	NM_001321350.2	MANE Select	c.-681C>T		5_prime_UTR	Exon 1 of 15	NP_001308279.1	F5H5K1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC37B	ENST00000543378.7	TSL:2 MANE Select	c.-681C>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 15	ENSP00000443345.2	F5H5K1
	LRRC37B	ENST00000543378.7	TSL:2 MANE Select	c.-681C>T		5_prime_UTR	Exon 1 of 15	ENSP00000443345.2	F5H5K1
	LRRC37B	ENST00000941835.1		c.-681C>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 15	ENSP00000611894.1

Frequencies

GnomAD3 genomes AF: 0.00162 AC: 245 AN: 151344 Hom.: 2 Cov.: 32

Gnomad AFR AF: 0.000145

Gnomad AMI AF: 0.0231

Gnomad AMR AF: 0.000263

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00550

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00230

Gnomad OTH AF: 0.000479

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

GnomAD4 genome AF: 0.00162 AC: 245 AN: 151452 Hom.: 2 Cov.: 32 AF XY: 0.00170 AC XY: 126 AN XY: 74012

African (AFR) AF: 0.000145 AC: 6 AN: 41448

American (AMR) AF: 0.000263 AC: 4 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3464

East Asian (EAS) AF: 0.00 AC: 0 AN: 5134

South Asian (SAS) AF: 0.00 AC: 0 AN: 4828

European-Finnish (FIN) AF: 0.00550 AC: 57 AN: 10358

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.00230 AC: 156 AN: 67686

Other (OTH) AF: 0.000474 AC: 1 AN: 2108

Alfa AF: 0.00221 Hom.: 0

Bravo AF: 0.00125

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	14
DANN	Benign	0.76
PhyloP100		-0.73
PromoterAI		-0.0054	Neutral

Splicing

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

Other links and lift over

dbSNP: rs544987121; hg19: chr17-30334661;