9-34164377-A-G

Variant names:

• chr9-34164377-A-G
• rs10971969

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 0.126 in 146,912 control chromosomes in the GnomAD database, including 1,487 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 0.13 (1487 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.199
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.126 AC: 18463 AN: 146888 Hom.: 1487 Cov.: 30

Gnomad AFR AF: 0.0343

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.00559

Gnomad SAS AF: 0.0640

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.125

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.126 AC: 18452 AN: 146912 Hom.: 1487 Cov.: 30 AF XY: 0.122 AC XY: 8710 AN XY: 71252

African (AFR) AF: 0.0343 AC: 1356 AN: 39578

American (AMR) AF: 0.132 AC: 1938 AN: 14654

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 567 AN: 3444

East Asian (EAS) AF: 0.00541 AC: 27 AN: 4994

South Asian (SAS) AF: 0.0635 AC: 298 AN: 4694

European-Finnish (FIN) AF: 0.182 AC: 1673 AN: 9180

Middle Eastern (MID) AF: 0.130 AC: 35 AN: 270

European-Non Finnish (NFE) AF: 0.180 AC: 12110 AN: 67160

Other (OTH) AF: 0.130 AC: 265 AN: 2032

Alfa AF: 0.136 Hom.: 348

Bravo AF: 0.116

Asia WGS AF: 0.0330 AC: 117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	7.1
DANN	Benign	0.87
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs10971969; hg19: chr9-34164375; COSMIC: COSV53375528;