2-71154810-A-T

Position:

• chr2-71154810-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 0.852 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.705

Gnomad4 AMR AF: 0.920

Gnomad4 ASJ AF: 0.955

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.960

Gnomad4 FIN AF: 0.894

Gnomad4 NFE AF: 0.895

Gnomad4 OTH AF: 0.868

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs357729; hg19: chr2-71381940;