rs16924434

Variant names:

• chr9-6358334-A-G
• rs16924434

Your query was ambiguous. Multiple possible variants found:

• chr9-6358334-A-G
• chr9-6358334-A-T

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 0.108 in 152,198 control chromosomes in the GnomAD database, including 1,225 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 0.11 (1225 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.571
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.276 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: 0.108 AC: 16495 AN: 152080 Hom.: 1228 Cov.: 32

Gnomad AFR AF: 0.0231

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.0985

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.108 AC: 16486 AN: 152198 Hom.: 1225 Cov.: 32 AF XY: 0.115 AC XY: 8550 AN XY: 74394

African (AFR) AF: 0.0231 AC: 959 AN: 41560

American (AMR) AF: 0.172 AC: 2623 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0985 AC: 342 AN: 3472

East Asian (EAS) AF: 0.288 AC: 1486 AN: 5162

South Asian (SAS) AF: 0.166 AC: 799 AN: 4818

European-Finnish (FIN) AF: 0.171 AC: 1809 AN: 10590

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8125 AN: 68000

Other (OTH) AF: 0.118 AC: 249 AN: 2110

Alfa AF: 0.114 Hom.: 367

Bravo AF: 0.103

Asia WGS AF: 0.188 AC: 653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	15
DANN	Benign	0.47
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs16924434; hg19: chr9-6358334;