rs10499006

Variant names:

• chr6-95845606-C-T
• rs10499006

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 0.504 in 151,902 control chromosomes in the GnomAD database, including 20,272 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 0.50 (20272 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76497 AN: 151784 Hom.: 20239 Cov.: 31

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.504 AC: 76571 AN: 151902 Hom.: 20272 Cov.: 31 AF XY: 0.499 AC XY: 37025 AN XY: 74220

African (AFR) AF: 0.383 AC: 15878 AN: 41424

American (AMR) AF: 0.532 AC: 8102 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1825 AN: 3468

East Asian (EAS) AF: 0.173 AC: 891 AN: 5158

South Asian (SAS) AF: 0.519 AC: 2504 AN: 4824

European-Finnish (FIN) AF: 0.525 AC: 5534 AN: 10532

Middle Eastern (MID) AF: 0.411 AC: 120 AN: 292

European-Non Finnish (NFE) AF: 0.591 AC: 40134 AN: 67946

Other (OTH) AF: 0.493 AC: 1038 AN: 2106

Alfa AF: 0.559 Hom.: 70484

Bravo AF: 0.494

Asia WGS AF: 0.332 AC: 1160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.33
DANN	Benign	0.52
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs10499006; hg19: chr6-96293482;