chr2-67957226-G-T

Variant names:

• chr2-67957226-G-T
• rs1503230

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 0.34 in 151,810 control chromosomes in the GnomAD database, including 8,977 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 0.34 (8977 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.364 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: 0.340 AC: 51572 AN: 151690 Hom.: 8964 Cov.: 31

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.340 AC: 51625 AN: 151810 Hom.: 8977 Cov.: 31 AF XY: 0.339 AC XY: 25129 AN XY: 74156

African (AFR) AF: 0.362 AC: 14965 AN: 41384

American (AMR) AF: 0.372 AC: 5659 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1236 AN: 3466

East Asian (EAS) AF: 0.140 AC: 723 AN: 5154

South Asian (SAS) AF: 0.314 AC: 1507 AN: 4806

European-Finnish (FIN) AF: 0.349 AC: 3689 AN: 10568

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.334 AC: 22693 AN: 67900

Other (OTH) AF: 0.367 AC: 775 AN: 2110

Alfa AF: 0.246 Hom.: 626

Bravo AF: 0.340

Asia WGS AF: 0.288 AC: 999 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.43
DANN	Benign	0.82
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs1503230; hg19: chr2-68184358; COSMIC: COSV107164947;