chr2-173656446-G-A

Variant names:

• chr2-173656446-G-A
• rs11691765
• ENST00000737367.1:n.392-105133G>A

Variant summary

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

The ENST00000737367.1(ENSG00000270460):​n.392-105133G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 152,126 control chromosomes in the GnomAD database, including 22,672 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 0.50 (22672 hom., cov: 33)
• Consequence: ENSG00000270460 ENST00000737367.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.224
• Publications: 3 publications found

Genes affected

ENSG00000270460 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000737367.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000270460	ENST00000737367.1		n.392-105133G>A		intron	N/A
	ENSG00000270460	ENST00000737368.1		n.519-105133G>A		intron	N/A
	ENSG00000270460	ENST00000737369.1		n.503+123107G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75395 AN: 152004 Hom.: 22670 Cov.: 33

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.723

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.496 AC: 75409 AN: 152126 Hom.: 22672 Cov.: 33 AF XY: 0.493 AC XY: 36705 AN XY: 74388

African (AFR) AF: 0.170 AC: 7046 AN: 41488

American (AMR) AF: 0.587 AC: 8971 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1877 AN: 3470

East Asian (EAS) AF: 0.138 AC: 713 AN: 5182

South Asian (SAS) AF: 0.475 AC: 2289 AN: 4822

European-Finnish (FIN) AF: 0.648 AC: 6852 AN: 10574

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.673 AC: 45761 AN: 67980

Other (OTH) AF: 0.519 AC: 1095 AN: 2110

Alfa AF: 0.616 Hom.: 15554

Bravo AF: 0.479

Asia WGS AF: 0.314 AC: 1093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.9
DANN	Benign	0.72
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs11691765; hg19: chr2-174521174;