rs9831754

Variant names:

• chr3-78304441-T-G
• rs9831754

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 0.199 in 152,018 control chromosomes in the GnomAD database, including 3,687 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 0.20 (3687 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.424 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: 0.199 AC: 30209 AN: 151904 Hom.: 3672 Cov.: 32

Gnomad AFR AF: 0.0931

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.199 AC: 30235 AN: 152018 Hom.: 3687 Cov.: 32 AF XY: 0.204 AC XY: 15193 AN XY: 74308

African (AFR) AF: 0.0929 AC: 3856 AN: 41522

American (AMR) AF: 0.283 AC: 4327 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 483 AN: 3466

East Asian (EAS) AF: 0.439 AC: 2253 AN: 5136

South Asian (SAS) AF: 0.268 AC: 1291 AN: 4816

European-Finnish (FIN) AF: 0.287 AC: 3028 AN: 10558

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14476 AN: 67934

Other (OTH) AF: 0.166 AC: 351 AN: 2114

Alfa AF: 0.211 Hom.: 6563

Bravo AF: 0.195

Asia WGS AF: 0.326 AC: 1129 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	10
DANN	Benign	0.78
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs9831754; hg19: chr3-78353591;