rs4632004

Variant names:

• chr13-105066291-C-A
• rs4632004

Your query was ambiguous. Multiple possible variants found:

• chr13-105066291-C-A
• chr13-105066291-C-G

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 0.691 in 151,974 control chromosomes in the GnomAD database, including 37,247 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 0.69 (37247 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.911 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: 0.691 AC: 104872 AN: 151856 Hom.: 37208 Cov.: 31

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.786

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.933

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.691 AC: 104954 AN: 151974 Hom.: 37247 Cov.: 31 AF XY: 0.694 AC XY: 51544 AN XY: 74268

African (AFR) AF: 0.845 AC: 35036 AN: 41482

American (AMR) AF: 0.545 AC: 8322 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.625 AC: 2165 AN: 3466

East Asian (EAS) AF: 0.933 AC: 4805 AN: 5152

South Asian (SAS) AF: 0.767 AC: 3698 AN: 4822

European-Finnish (FIN) AF: 0.679 AC: 7168 AN: 10554

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.610 AC: 41433 AN: 67916

Other (OTH) AF: 0.673 AC: 1420 AN: 2110

Alfa AF: 0.619 Hom.: 44045

Bravo AF: 0.686

Asia WGS AF: 0.828 AC: 2881 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	1.2
DANN	Benign	0.40
PhyloP100		-0.031

Splicing

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

Other links and lift over

dbSNP: rs4632004; hg19: chr13-105718642;