2-237917167-C-T

Variant names:

• chr2-237917167-C-T
• rs6729271

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 0.577 in 151,968 control chromosomes in the GnomAD database, including 26,563 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 (26563 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270
• Publications: 4 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 = 0.733 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: 0.577 AC: 87562 AN: 151850 Hom.: 26517 Cov.: 32

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.577 AC: 87659 AN: 151968 Hom.: 26563 Cov.: 32 AF XY: 0.572 AC XY: 42448 AN XY: 74272

African (AFR) AF: 0.740 AC: 30664 AN: 41456

American (AMR) AF: 0.430 AC: 6560 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2225 AN: 3468

East Asian (EAS) AF: 0.267 AC: 1375 AN: 5158

South Asian (SAS) AF: 0.493 AC: 2375 AN: 4816

European-Finnish (FIN) AF: 0.575 AC: 6053 AN: 10530

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.537 AC: 36497 AN: 67970

Other (OTH) AF: 0.569 AC: 1198 AN: 2104

Alfa AF: 0.549 Hom.: 78385

Bravo AF: 0.570

Asia WGS AF: 0.411 AC: 1430 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	3.3
DANN	Benign	0.45
PhyloP100		0.027

Splicing

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

Other links and lift over

dbSNP: rs6729271; hg19: chr2-238825809;