2-161039641-T-C

Position:

• chr2-161039641-T-C

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 0.869 in 152,196 control chromosomes in the GnomAD database, including 57,517 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 0.87 (57517 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 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: 0.869 AC: 132125 AN: 152078 Hom.: 57480 Cov.: 32

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.889

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.867

Gnomad FIN AF: 0.859

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.889

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.869 AC: 132216 AN: 152196 Hom.: 57517 Cov.: 32 AF XY: 0.868 AC XY: 64584 AN XY: 74388

Gnomad4 AFR AF: 0.822

Gnomad4 AMR AF: 0.889

Gnomad4 ASJ AF: 0.842

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.867

Gnomad4 FIN AF: 0.859

Gnomad4 NFE AF: 0.889

Gnomad4 OTH AF: 0.847

Alfa AF: 0.883 Hom.: 22562

Bravo AF: 0.871

Asia WGS AF: 0.920 AC: 3193 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	7.0
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs197275; hg19: chr2-161896152;