chr2-151068269-T-C

Variant names:

• chr2-151068269-T-C
• rs1485120

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 0.934 in 152,226 control chromosomes in the GnomAD database, including 67,038 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 0.93 (67038 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.991 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: 0.934 AC: 142070 AN: 152108 Hom.: 67003 Cov.: 31

Gnomad AFR AF: 0.784

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.970

Gnomad ASJ AF: 0.993

Gnomad EAS AF: 0.985

Gnomad SAS AF: 0.957

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.997

Gnomad OTH AF: 0.939

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

GnomAD4 genome AF: 0.934 AC: 142157 AN: 152226 Hom.: 67038 Cov.: 31 AF XY: 0.935 AC XY: 69560 AN XY: 74416

African (AFR) AF: 0.784 AC: 32513 AN: 41492

American (AMR) AF: 0.970 AC: 14838 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.993 AC: 3448 AN: 3472

East Asian (EAS) AF: 0.985 AC: 5090 AN: 5170

South Asian (SAS) AF: 0.958 AC: 4623 AN: 4828

European-Finnish (FIN) AF: 1.00 AC: 10618 AN: 10622

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.997 AC: 67844 AN: 68032

Other (OTH) AF: 0.939 AC: 1986 AN: 2114

Alfa AF: 0.951 Hom.: 8974

Bravo AF: 0.925

Asia WGS AF: 0.955 AC: 3320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.34
DANN	Benign	0.24
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1485120; hg19: chr2-151924783;