2-237917167-C-T

Position:

• chr2-237917167-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.740

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.642

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.537

Gnomad4 OTH AF: 0.569

Alfa AF: 0.541 Hom.: 47158

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6729271; hg19: chr2-238825809;