rs9604365

Variant names:

• chr13-111922883-G-A
• rs9604365

Your query was ambiguous. Multiple possible variants found:

• chr13-111922883-G-A
• chr13-111922883-G-C

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 0.829 in 152,142 control chromosomes in the GnomAD database, including 54,530 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 0.83 (54530 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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: 0.830 AC: 126128 AN: 152024 Hom.: 54519 Cov.: 32

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.970

Gnomad AMR AF: 0.904

Gnomad ASJ AF: 0.931

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.925

Gnomad FIN AF: 0.920

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.938

Gnomad OTH AF: 0.848

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

GnomAD4 genome AF: 0.829 AC: 126176 AN: 152142 Hom.: 54530 Cov.: 32 AF XY: 0.832 AC XY: 61867 AN XY: 74374

African (AFR) AF: 0.555 AC: 23017 AN: 41446

American (AMR) AF: 0.904 AC: 13833 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.931 AC: 3231 AN: 3472

East Asian (EAS) AF: 0.997 AC: 5147 AN: 5162

South Asian (SAS) AF: 0.925 AC: 4462 AN: 4822

European-Finnish (FIN) AF: 0.920 AC: 9750 AN: 10602

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.938 AC: 63801 AN: 68022

Other (OTH) AF: 0.849 AC: 1793 AN: 2112

Alfa AF: 0.903 Hom.: 79872

Bravo AF: 0.818

Asia WGS AF: 0.933 AC: 3246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.13
DANN	Benign	0.71
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs9604365; hg19: chr13-112577197;