rs2191265

Variant names:

• chr7-12865442-A-G
• rs2191265
• ENST00000638964.1:n.484+62710A>G

Variant summary

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

The ENST00000638964.1(ENSG00000229618):​n.484+62710A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 151,904 control chromosomes in the GnomAD database, including 23,539 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 0.54 (23539 hom., cov: 31)
• Consequence: ENSG00000229618 ENST00000638964.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• Publications: 1 publications found

Genes affected

ENSG00000229618 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000638964.1. 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
	ENSG00000229618	ENST00000638964.1	TSL:5	n.484+62710A>G		intron	N/A
	ENSG00000229618	ENST00000639998.1	TSL:5	n.483+107126A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82367 AN: 151786 Hom.: 23518 Cov.: 31

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.543 AC: 82421 AN: 151904 Hom.: 23539 Cov.: 31 AF XY: 0.543 AC XY: 40313 AN XY: 74238

African (AFR) AF: 0.747 AC: 30928 AN: 41430

American (AMR) AF: 0.487 AC: 7436 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1571 AN: 3468

East Asian (EAS) AF: 0.481 AC: 2458 AN: 5106

South Asian (SAS) AF: 0.466 AC: 2244 AN: 4816

European-Finnish (FIN) AF: 0.492 AC: 5198 AN: 10568

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 31005 AN: 67938

Other (OTH) AF: 0.541 AC: 1137 AN: 2102

Alfa AF: 0.510 Hom.: 3606

Bravo AF: 0.548

Asia WGS AF: 0.530 AC: 1844 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	1.6
DANN	Benign	0.29
PhyloP100		-0.79

Splicing

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: rs2191265;

hg19: chr7-12905067;