9-31147842-C-A

Position:

• chr9-31147842-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.953 in 151,870 control chromosomes in the GnomAD database, including 69,094 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 0.95 (69094 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.953 AC: 144591 AN: 151752 Hom.: 69045 Cov.: 31

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.975

Gnomad ASJ AF: 0.978

Gnomad EAS AF: 0.952

Gnomad SAS AF: 0.969

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.983

Gnomad OTH AF: 0.956

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

GnomAD4 genome AF: 0.953 AC: 144696 AN: 151870 Hom.: 69094 Cov.: 31 AF XY: 0.954 AC XY: 70814 AN XY: 74234

Gnomad4 AFR AF: 0.878

Gnomad4 AMR AF: 0.975

Gnomad4 ASJ AF: 0.978

Gnomad4 EAS AF: 0.952

Gnomad4 SAS AF: 0.969

Gnomad4 FIN AF: 0.999

Gnomad4 NFE AF: 0.983

Gnomad4 OTH AF: 0.956

Alfa AF: 0.971 Hom.: 11703

Bravo AF: 0.948

Asia WGS AF: 0.952 AC: 3300 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.70
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1335159; hg19: chr9-31147840;