chr13-42335277-A-G

Variant names:

• chr13-42335277-A-G
• rs9525610

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 0.119 in 152,218 control chromosomes in the GnomAD database, including 1,127 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 0.12 (1127 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.437
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.179 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: 0.119 AC: 18080 AN: 152100 Hom.: 1127 Cov.: 33

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.0817

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.119 AC: 18083 AN: 152218 Hom.: 1127 Cov.: 33 AF XY: 0.120 AC XY: 8965 AN XY: 74434

African (AFR) AF: 0.136 AC: 5660 AN: 41528

American (AMR) AF: 0.0815 AC: 1247 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 406 AN: 3466

East Asian (EAS) AF: 0.175 AC: 903 AN: 5174

South Asian (SAS) AF: 0.189 AC: 910 AN: 4818

European-Finnish (FIN) AF: 0.117 AC: 1245 AN: 10610

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7290 AN: 67998

Other (OTH) AF: 0.128 AC: 271 AN: 2114

Alfa AF: 0.0530 Hom.: 60

Bravo AF: 0.115

Asia WGS AF: 0.203 AC: 707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.73
DANN	Benign	0.30
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs9525610; hg19: chr13-42909413;