rs602618

chr10-111083327-C-Achr10-111083327-C-T

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 0.582 in 152,086 control chromosomes in the GnomAD database, including 28,550 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 0.58 (28550 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.339

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.723 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: 0.583 AC: 88570 AN: 151968 Hom.: 28562 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.729

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.582 AC: 88577 AN: 152086 Hom.: 28550 Cov.: 32 AF XY: 0.580 AC XY: 43105 AN XY: 74344

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.720

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.741

Gnomad4 NFE AF: 0.729

Gnomad4 OTH AF: 0.591

Alfa AF: 0.698 Hom.: 50243

Bravo AF: 0.565

Asia WGS AF: 0.367 AC: 1277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.42
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs602618; hg19: chr10-112843085;