rs2316757

Variant names:

• chr17-46988859-A-G
• rs2316757
• ENST00000571841.1:n.676+22233A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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]

ENSG00000262879 (HGNC:58690):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000571841.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000262633	ENST00000571841.1	TSL:5	n.676+22233A>G		intron	N/A	ENSP00000461460.1	E7EQ34
	ENSG00000291209	ENST00000570478.6	TSL:4	n.291+10088A>G		intron	N/A
	ENSG00000262879	ENST00000575930.5	TSL:5	n.661-4790T>C		intron	N/A

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

African (AFR) AF: 0.670 AC: 27779 AN: 41482

American (AMR) AF: 0.633 AC: 9663 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.833 AC: 2891 AN: 3472

East Asian (EAS) AF: 0.384 AC: 1980 AN: 5158

South Asian (SAS) AF: 0.732 AC: 3527 AN: 4818

European-Finnish (FIN) AF: 0.657 AC: 6935 AN: 10556

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.753 AC: 51226 AN: 67992

Other (OTH) AF: 0.708 AC: 1496 AN: 2114

Alfa AF: 0.704 Hom.: 6920

Bravo AF: 0.692

Asia WGS AF: 0.581 AC: 2022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.70
DANN	Benign	0.33
PhyloP100		0.072
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2316757;

hg19: chr17-45066225;