10-5996890-G-C

Variant names:

• chr10-5996890-G-C
• rs6602364

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.415 AC: 17164 AN: 41366

American (AMR) AF: 0.494 AC: 7539 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1924 AN: 3472

East Asian (EAS) AF: 0.699 AC: 3596 AN: 5146

South Asian (SAS) AF: 0.475 AC: 2283 AN: 4810

European-Finnish (FIN) AF: 0.441 AC: 4645 AN: 10532

Middle Eastern (MID) AF: 0.527 AC: 154 AN: 292

European-Non Finnish (NFE) AF: 0.555 AC: 37670 AN: 67930

Other (OTH) AF: 0.516 AC: 1088 AN: 2110

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
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs6602364; hg19: chr10-6038853;