rs10517985

chr4-66557799-G-A

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 0.108 in 152,088 control chromosomes in the GnomAD database, including 2,496 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 0.11 (2496 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.335 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: 0.108 AC: 16337 AN: 151970 Hom.: 2484 Cov.: 33

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.0724

Gnomad ASJ AF: 0.0334

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0118

Gnomad FIN AF: 0.00832

Gnomad MID AF: 0.0255

Gnomad NFE AF: 0.00944

Gnomad OTH AF: 0.0960

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

GnomAD4 genome AF: 0.108 AC: 16382 AN: 152088 Hom.: 2496 Cov.: 33 AF XY: 0.104 AC XY: 7735 AN XY: 74370

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.0722

Gnomad4 ASJ AF: 0.0334

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0116

Gnomad4 FIN AF: 0.00832

Gnomad4 NFE AF: 0.00944

Gnomad4 OTH AF: 0.0950

Alfa AF: 0.0778 Hom.: 463

Bravo AF: 0.122

Asia WGS AF: 0.0290 AC: 102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
Cadd	Benign	9.1
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517985; hg19: chr4-67423517;