2-68418428-T-G

Variant names:

• chr2-68418428-T-G
• rs10167650

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 0.314 in 152,134 control chromosomes in the GnomAD database, including 8,391 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 0.31 (8391 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 13 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 (EAS) allele frequency at 95% confidence interval = 0.706 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: 0.314 AC: 47692 AN: 152016 Hom.: 8393 Cov.: 33

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.314 AC: 47715 AN: 152134 Hom.: 8391 Cov.: 33 AF XY: 0.322 AC XY: 23926 AN XY: 74392

African (AFR) AF: 0.293 AC: 12131 AN: 41472

American (AMR) AF: 0.446 AC: 6813 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1221 AN: 3472

East Asian (EAS) AF: 0.725 AC: 3759 AN: 5184

South Asian (SAS) AF: 0.514 AC: 2478 AN: 4824

European-Finnish (FIN) AF: 0.264 AC: 2797 AN: 10576

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17401 AN: 67994

Other (OTH) AF: 0.320 AC: 676 AN: 2114

Alfa AF: 0.135 Hom.: 222

Bravo AF: 0.328

Asia WGS AF: 0.566 AC: 1967 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	0.53
DANN	Benign	0.43
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10167650; hg19: chr2-68645560;