2-68419963-C-T

Variant names:

• chr2-68419963-C-T
• rs7595037

Variant summary

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

The variant allele was found at a frequency of 0.58 in 151,920 control chromosomes in the GnomAD database, including 26,161 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 0.58 (26161 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.191
• Publications: 39 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.579 AC: 87944 AN: 151804 Hom.: 26114 Cov.: 30

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.580 AC: 88045 AN: 151920 Hom.: 26161 Cov.: 30 AF XY: 0.587 AC XY: 43582 AN XY: 74260

African (AFR) AF: 0.524 AC: 21696 AN: 41394

American (AMR) AF: 0.690 AC: 10553 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.694 AC: 2407 AN: 3466

East Asian (EAS) AF: 0.900 AC: 4642 AN: 5160

South Asian (SAS) AF: 0.745 AC: 3589 AN: 4816

European-Finnish (FIN) AF: 0.541 AC: 5702 AN: 10534

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.551 AC: 37433 AN: 67946

Other (OTH) AF: 0.619 AC: 1306 AN: 2110

Alfa AF: 0.573 Hom.: 114348

Bravo AF: 0.589

Asia WGS AF: 0.814 AC: 2831 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.1
DANN	Benign	0.43
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs7595037; hg19: chr2-68647095;