rs9308868

chr2-103744962-G-A

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 0.455 in 151,840 control chromosomes in the GnomAD database, including 16,685 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 0.45 (16685 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.78

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.7 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: 0.455 AC: 69033 AN: 151722 Hom.: 16675 Cov.: 31

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.455 AC: 69065 AN: 151840 Hom.: 16685 Cov.: 31 AF XY: 0.459 AC XY: 34031 AN XY: 74180

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.574

Gnomad4 EAS AF: 0.651

Gnomad4 SAS AF: 0.720

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.440

Alfa AF: 0.509 Hom.: 33071

Bravo AF: 0.435

Asia WGS AF: 0.665 AC: 2312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.0090
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9308868; hg19: chr2-104361420;