2-67888895-A-G

Variant names:

• chr2-67888895-A-G
• rs7595509

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.859 in 152,140 control chromosomes in the GnomAD database, including 56,835 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 0.86 (56835 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.859 AC: 130563 AN: 152022 Hom.: 56777 Cov.: 31

Gnomad AFR AF: 0.955

Gnomad AMI AF: 0.989

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.872

Gnomad EAS AF: 0.782

Gnomad SAS AF: 0.816

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.857

Gnomad OTH AF: 0.854

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

GnomAD4 genome AF: 0.859 AC: 130671 AN: 152140 Hom.: 56835 Cov.: 31 AF XY: 0.851 AC XY: 63326 AN XY: 74370

African (AFR) AF: 0.955 AC: 39635 AN: 41510

American (AMR) AF: 0.663 AC: 10119 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.872 AC: 3027 AN: 3472

East Asian (EAS) AF: 0.784 AC: 4029 AN: 5142

South Asian (SAS) AF: 0.815 AC: 3930 AN: 4820

European-Finnish (FIN) AF: 0.821 AC: 8694 AN: 10594

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.857 AC: 58267 AN: 68020

Other (OTH) AF: 0.857 AC: 1808 AN: 2110

Alfa AF: 0.853 Hom.: 79966

Bravo AF: 0.849

Asia WGS AF: 0.786 AC: 2734 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	16
DANN	Benign	0.69
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs7595509; hg19: chr2-68116027;