9-4941997-G-C

Variant names:

• chr9-4941997-G-C
• rs3968

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 0.739 in 151,966 control chromosomes in the GnomAD database, including 42,222 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 0.74 (42222 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112290 AN: 151846 Hom.: 42205 Cov.: 31

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.807

Gnomad ASJ AF: 0.818

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.776

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

GnomAD4 genome AF: 0.739 AC: 112349 AN: 151966 Hom.: 42222 Cov.: 31 AF XY: 0.737 AC XY: 54734 AN XY: 74292

African (AFR) AF: 0.597 AC: 24740 AN: 41414

American (AMR) AF: 0.808 AC: 12338 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.818 AC: 2840 AN: 3470

East Asian (EAS) AF: 0.664 AC: 3432 AN: 5172

South Asian (SAS) AF: 0.634 AC: 3056 AN: 4818

European-Finnish (FIN) AF: 0.772 AC: 8155 AN: 10566

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.814 AC: 55313 AN: 67944

Other (OTH) AF: 0.770 AC: 1621 AN: 2106

Alfa AF: 0.764 Hom.: 5285

Bravo AF: 0.738

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.49
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs3968; hg19: chr9-4941997;