2-67960000-C-G

Variant names:

• chr2-67960000-C-G
• rs6751663

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 0.519 in 151,858 control chromosomes in the GnomAD database, including 20,755 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 0.52 (20755 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.568 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: 0.519 AC: 78702 AN: 151740 Hom.: 20734 Cov.: 31

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.519 AC: 78771 AN: 151858 Hom.: 20755 Cov.: 31 AF XY: 0.513 AC XY: 38079 AN XY: 74206

African (AFR) AF: 0.574 AC: 23792 AN: 41444

American (AMR) AF: 0.520 AC: 7928 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1756 AN: 3462

East Asian (EAS) AF: 0.263 AC: 1354 AN: 5140

South Asian (SAS) AF: 0.485 AC: 2338 AN: 4816

European-Finnish (FIN) AF: 0.438 AC: 4623 AN: 10544

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.521 AC: 35345 AN: 67904

Other (OTH) AF: 0.514 AC: 1084 AN: 2110

Alfa AF: 0.394 Hom.: 1009

Bravo AF: 0.524

Asia WGS AF: 0.447 AC: 1555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.71
PhyloP100		-0.053

Splicing

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

Other links and lift over

dbSNP: rs6751663; hg19: chr2-68187132;