chr6-104334470-C-G

Variant names:

• chr6-104334470-C-G
• rs10499040

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 0.12 in 151,946 control chromosomes in the GnomAD database, including 1,328 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 0.12 (1328 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.296 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: 0.120 AC: 18223 AN: 151828 Hom.: 1325 Cov.: 32

Gnomad AFR AF: 0.0628

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.120 AC: 18232 AN: 151946 Hom.: 1328 Cov.: 32 AF XY: 0.125 AC XY: 9289 AN XY: 74258

African (AFR) AF: 0.0628 AC: 2601 AN: 41448

American (AMR) AF: 0.161 AC: 2450 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 666 AN: 3468

East Asian (EAS) AF: 0.309 AC: 1591 AN: 5154

South Asian (SAS) AF: 0.206 AC: 991 AN: 4806

European-Finnish (FIN) AF: 0.123 AC: 1301 AN: 10554

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8060 AN: 67956

Other (OTH) AF: 0.144 AC: 303 AN: 2110

Alfa AF: 0.118 Hom.: 143

Bravo AF: 0.121

Asia WGS AF: 0.231 AC: 805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.40
DANN	Benign	0.65
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10499040; hg19: chr6-104782345; COSMIC: COSV107166699;