2-156949941-A-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 0.251 in 151,982 control chromosomes in the GnomAD database, including 6,968 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 0.25 (6968 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38086 AN: 151864 Hom.: 6947 Cov.: 32

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.251 AC: 38146 AN: 151982 Hom.: 6968 Cov.: 32 AF XY: 0.252 AC XY: 18709 AN XY: 74298

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.246

Alfa AF: 0.176 Hom.: 455

Bravo AF: 0.270

Asia WGS AF: 0.223 AC: 775 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.37
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1033224; hg19: chr2-157806453;