rs10517604

Variant names:

• chr4-154864506-C-T
• rs10517604

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 0.103 in 152,152 control chromosomes in the GnomAD database, including 2,409 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 0.10 (2409 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.331 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: 0.103 AC: 15652 AN: 152034 Hom.: 2394 Cov.: 32

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0512

Gnomad ASJ AF: 0.0320

Gnomad EAS AF: 0.0119

Gnomad SAS AF: 0.0122

Gnomad FIN AF: 0.00595

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.00707

Gnomad OTH AF: 0.0927

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

GnomAD4 genome AF: 0.103 AC: 15703 AN: 152152 Hom.: 2409 Cov.: 32 AF XY: 0.100 AC XY: 7443 AN XY: 74392

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.0511

Gnomad4 ASJ AF: 0.0320

Gnomad4 EAS AF: 0.0120

Gnomad4 SAS AF: 0.0120

Gnomad4 FIN AF: 0.00595

Gnomad4 NFE AF: 0.00707

Gnomad4 OTH AF: 0.0918

Alfa AF: 0.0616 Hom.: 175

Bravo AF: 0.116

Asia WGS AF: 0.0360 AC: 124 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	0.26
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517604; hg19: chr4-155785658;