6-104334470-C-G

Variant names:

• chr6-104334470-C-G
• rs10499040

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 0.12 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.120 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

Gnomad4 AFR AF: 0.0628

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.309

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.144

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10499040; hg19: chr6-104782345;