rs16931419

Variant names:

• chr9-129735271-T-C
• rs16931419

Your query was ambiguous. Multiple possible variants found:

• chr9-129735271-T-C
• chr9-129735271-T-G

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 0.223 in 152,144 control chromosomes in the GnomAD database, including 5,107 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 0.22 (5107 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.190
• Publications: 3 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 = 0.422 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: 0.223 AC: 33972 AN: 152026 Hom.: 5104 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.223 AC: 34001 AN: 152144 Hom.: 5107 Cov.: 32 AF XY: 0.219 AC XY: 16322 AN XY: 74382

African (AFR) AF: 0.427 AC: 17726 AN: 41490

American (AMR) AF: 0.144 AC: 2203 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 603 AN: 3470

East Asian (EAS) AF: 0.194 AC: 998 AN: 5150

South Asian (SAS) AF: 0.172 AC: 832 AN: 4830

European-Finnish (FIN) AF: 0.108 AC: 1143 AN: 10622

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9661 AN: 67966

Other (OTH) AF: 0.214 AC: 451 AN: 2112

Alfa AF: 0.167 Hom.: 9188

Bravo AF: 0.236

Asia WGS AF: 0.191 AC: 664 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	0.48
DANN	Benign	0.62
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs16931419; hg19: chr9-132497550;