rs1335159

Variant names:

• chr9-31147842-C-A
• rs1335159

Your query was ambiguous. Multiple possible variants found:

• chr9-31147842-C-A
• chr9-31147842-C-G
• chr9-31147842-C-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 0.953 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.878 AC: 36434 AN: 41482

American (AMR) AF: 0.975 AC: 14838 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.978 AC: 3392 AN: 3468

East Asian (EAS) AF: 0.952 AC: 4931 AN: 5180

South Asian (SAS) AF: 0.969 AC: 4667 AN: 4816

European-Finnish (FIN) AF: 0.999 AC: 10611 AN: 10618

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.983 AC: 66611 AN: 67766

Other (OTH) AF: 0.956 AC: 2018 AN: 2110

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1335159; hg19: chr9-31147840;