rs2316757

Positions:

• chr17-46988859-A-G
• chr17-46988859-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000571841.1(ENSG00000262633):​n.676+22233A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 152,064 control chromosomes in the GnomAD database, including 37,869 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 0.70 (37869 hom., cov: 32)
• Consequence: ENSG00000262633 ENST00000571841.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720

Genes affected

ENSG00000262633 (HGNC:):

LRRC37A2 (HGNC:32404): (leucine rich repeat containing 37 member A2) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.748 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRRC37A2	XM_024450773.2	c.4810-60197A>G		intron_variant			XP_024306541.1
LOC101927060	XR_001753104.3	n.7775-2898T>C		intron_variant
LOC101927060	XR_001753124.3	n.5478-2898T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000262633	ENST00000571841.1	n.676+22233A>G		intron_variant		5		ENSP00000461460.1

Frequencies

GnomAD3 genomes AF: 0.700 AC: 106324 AN: 151946 Hom.: 37831 Cov.: 32

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.709

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

GnomAD4 genome AF: 0.700 AC: 106420 AN: 152064 Hom.: 37869 Cov.: 32 AF XY: 0.695 AC XY: 51654 AN XY: 74338

Gnomad4 AFR AF: 0.670

Gnomad4 AMR AF: 0.633

Gnomad4 ASJ AF: 0.833

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.732

Gnomad4 FIN AF: 0.657

Gnomad4 NFE AF: 0.753

Gnomad4 OTH AF: 0.708

Alfa AF: 0.705 Hom.: 6743

Bravo AF: 0.692

Asia WGS AF: 0.581 AC: 2022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.70
DANN	Benign	0.33

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

Publications

LitVar

Other links and lift over

dbSNP: rs2316757; hg19: chr17-45066225;