rs2697153

Variant names:

• chr3-10981986-G-A
• rs2697153

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 0.731 in 152,120 control chromosomes in the GnomAD database, including 42,150 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 0.73 (42150 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.922 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: 0.730 AC: 111002 AN: 152002 Hom.: 42085 Cov.: 32

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.805

Gnomad SAS AF: 0.858

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.718

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

GnomAD4 genome AF: 0.731 AC: 111128 AN: 152120 Hom.: 42150 Cov.: 32 AF XY: 0.734 AC XY: 54577 AN XY: 74350

Gnomad4 AFR AF: 0.930

Gnomad4 AMR AF: 0.761

Gnomad4 ASJ AF: 0.699

Gnomad4 EAS AF: 0.805

Gnomad4 SAS AF: 0.859

Gnomad4 FIN AF: 0.618

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.719

Alfa AF: 0.642 Hom.: 65268

Bravo AF: 0.750

Asia WGS AF: 0.832 AC: 2895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2697153; hg19: chr3-11023672;