rs10518617

Positions:

• chr4-132700670-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.00516

Gnomad4 AMR AF: 0.0889

Gnomad4 ASJ AF: 0.0168

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.0438

Gnomad4 FIN AF: 0.0293

Gnomad4 NFE AF: 0.0101

Gnomad4 OTH AF: 0.0234

Alfa AF: 0.0184 Hom.: 220

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10518617; hg19: chr4-133621825;