rs6602364

chr10-5996890-G-C

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 0.505 in 151,814 control chromosomes in the GnomAD database, including 19,960 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 0.51 (19960 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.68 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: 0.505 AC: 76648 AN: 151696 Hom.: 19937 Cov.: 30

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.505 AC: 76726 AN: 151814 Hom.: 19960 Cov.: 30 AF XY: 0.500 AC XY: 37136 AN XY: 74204

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.554

Gnomad4 EAS AF: 0.699

Gnomad4 SAS AF: 0.475

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.555

Gnomad4 OTH AF: 0.516

Alfa AF: 0.524 Hom.: 2633

Bravo AF: 0.504

Asia WGS AF: 0.605 AC: 2106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.0
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6602364; hg19: chr10-6038853;