rs3814113

Variant names:

• chr9-16915023-T-C
• rs3814113

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 0.413 in 151,824 control chromosomes in the GnomAD database, including 14,020 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 0.41 (14020 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 71 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 (AFR) allele frequency at 95% confidence interval = 0.544 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: 0.412 AC: 62570 AN: 151706 Hom.: 13995 Cov.: 31

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.413 AC: 62647 AN: 151824 Hom.: 14020 Cov.: 31 AF XY: 0.414 AC XY: 30719 AN XY: 74198

African (AFR) AF: 0.550 AC: 22774 AN: 41392

American (AMR) AF: 0.534 AC: 8135 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1363 AN: 3470

East Asian (EAS) AF: 0.282 AC: 1445 AN: 5132

South Asian (SAS) AF: 0.416 AC: 2002 AN: 4808

European-Finnish (FIN) AF: 0.305 AC: 3224 AN: 10554

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22208 AN: 67916

Other (OTH) AF: 0.417 AC: 880 AN: 2110

Alfa AF: 0.353 Hom.: 47373

Bravo AF: 0.434

Asia WGS AF: 0.405 AC: 1407 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	0.85
DANN	Benign	0.53
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs3814113; hg19: chr9-16915021; COSMIC: COSV53318135;