rs4517638

Variant names:

• chr13-105416860-G-A
• rs4517638

Your query was ambiguous. Multiple possible variants found:

• chr13-105416860-G-A
• chr13-105416860-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 0.0717 in 152,194 control chromosomes in the GnomAD database, including 462 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 0.072 (462 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.27
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0877 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: 0.0717 AC: 10902 AN: 152076 Hom.: 462 Cov.: 32

Gnomad AFR AF: 0.0240

Gnomad AMI AF: 0.0725

Gnomad AMR AF: 0.0591

Gnomad ASJ AF: 0.0855

Gnomad EAS AF: 0.0804

Gnomad SAS AF: 0.0834

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0896

Gnomad OTH AF: 0.0772

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

GnomAD4 genome AF: 0.0717 AC: 10910 AN: 152194 Hom.: 462 Cov.: 32 AF XY: 0.0752 AC XY: 5599 AN XY: 74412

African (AFR) AF: 0.0240 AC: 998 AN: 41570

American (AMR) AF: 0.0592 AC: 904 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0855 AC: 297 AN: 3472

East Asian (EAS) AF: 0.0802 AC: 415 AN: 5172

South Asian (SAS) AF: 0.0849 AC: 409 AN: 4818

European-Finnish (FIN) AF: 0.147 AC: 1553 AN: 10590

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0896 AC: 6090 AN: 67982

Other (OTH) AF: 0.0764 AC: 161 AN: 2108

Alfa AF: 0.0797 Hom.: 1105

Bravo AF: 0.0626

Asia WGS AF: 0.0770 AC: 268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.3
DANN	Benign	0.69
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs4517638; hg19: chr13-106069209;