rs9308868

Variant names:

• chr2-103744962-G-A
• rs9308868

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 0.455 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
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.297 AC: 12319 AN: 41438

American (AMR) AF: 0.414 AC: 6307 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1988 AN: 3464

East Asian (EAS) AF: 0.651 AC: 3342 AN: 5132

South Asian (SAS) AF: 0.720 AC: 3466 AN: 4816

European-Finnish (FIN) AF: 0.496 AC: 5207 AN: 10506

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.516 AC: 35017 AN: 67928

Other (OTH) AF: 0.440 AC: 929 AN: 2112

Alfa AF: 0.506 Hom.: 66044

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
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs9308868; hg19: chr2-104361420;