2-71154810-A-T

Variant names:

• chr2-71154810-A-T
• rs357729

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 0.852 in 152,192 control chromosomes in the GnomAD database, including 55,858 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 0.85 (55858 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.739
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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: 0.852 AC: 129564 AN: 152074 Hom.: 55830 Cov.: 33

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.920

Gnomad ASJ AF: 0.955

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.959

Gnomad FIN AF: 0.894

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.868

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

GnomAD4 genome AF: 0.852 AC: 129648 AN: 152192 Hom.: 55858 Cov.: 33 AF XY: 0.856 AC XY: 63711 AN XY: 74406

African (AFR) AF: 0.705 AC: 29238 AN: 41482

American (AMR) AF: 0.920 AC: 14081 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.955 AC: 3316 AN: 3472

East Asian (EAS) AF: 0.994 AC: 5133 AN: 5164

South Asian (SAS) AF: 0.960 AC: 4634 AN: 4828

European-Finnish (FIN) AF: 0.894 AC: 9482 AN: 10604

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.895 AC: 60855 AN: 68022

Other (OTH) AF: 0.868 AC: 1834 AN: 2112

Alfa AF: 0.864 Hom.: 6692

Bravo AF: 0.849

Asia WGS AF: 0.949 AC: 3299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.9
DANN	Benign	0.89
PhyloP100		0.74

Splicing

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

Other links and lift over

dbSNP: rs357729; hg19: chr2-71381940;