3-196591984-C-T

Variant names:

• chr3-196591984-C-T
• rs9843585

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 0.624 in 150,580 control chromosomes in the GnomAD database, including 29,433 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 0.62 (29433 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.782

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.713 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: 0.624 AC: 93862 AN: 150482 Hom.: 29401 Cov.: 27

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.624 AC: 93937 AN: 150580 Hom.: 29433 Cov.: 27 AF XY: 0.627 AC XY: 46123 AN XY: 73572

Gnomad4 AFR AF: 0.555

Gnomad4 AMR AF: 0.621

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.681

Gnomad4 SAS AF: 0.733

Gnomad4 FIN AF: 0.690

Gnomad4 NFE AF: 0.644

Gnomad4 OTH AF: 0.607

Alfa AF: 0.636 Hom.: 37440

Bravo AF: 0.612

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.21
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9843585; hg19: chr3-196318855;