rs10518617

Variant names:

• chr4-132700670-A-G
• rs10518617

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 0.0281 in 151,602 control chromosomes in the GnomAD database, including 295 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 0.028 (295 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.257 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: 0.0281 AC: 4251 AN: 151484 Hom.: 294 Cov.: 31

Gnomad AFR AF: 0.00518

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0885

Gnomad ASJ AF: 0.0168

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.0439

Gnomad FIN AF: 0.0293

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0101

Gnomad OTH AF: 0.0236

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

GnomAD4 genome AF: 0.0281 AC: 4255 AN: 151602 Hom.: 295 Cov.: 31 AF XY: 0.0320 AC XY: 2368 AN XY: 74114

African (AFR) AF: 0.00516 AC: 214 AN: 41474

American (AMR) AF: 0.0889 AC: 1349 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.0168 AC: 58 AN: 3462

East Asian (EAS) AF: 0.268 AC: 1381 AN: 5144

South Asian (SAS) AF: 0.0438 AC: 211 AN: 4822

European-Finnish (FIN) AF: 0.0293 AC: 310 AN: 10594

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0101 AC: 680 AN: 67626

Other (OTH) AF: 0.0234 AC: 49 AN: 2096

Alfa AF: 0.0187 Hom.: 332

Bravo AF: 0.0332

Asia WGS AF: 0.132 AC: 453 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.0
DANN	Benign	0.66
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs10518617; hg19: chr4-133621825;