rs10484347

Variant names:

• chr6-14013529-C-T
• rs10484347

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 0.104 in 152,066 control chromosomes in the GnomAD database, including 1,152 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 0.10 (1152 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.197 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: 0.104 AC: 15764 AN: 151950 Hom.: 1154 Cov.: 32

Gnomad AFR AF: 0.0269

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.0533

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.0649

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.0954

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

GnomAD4 genome AF: 0.104 AC: 15759 AN: 152066 Hom.: 1152 Cov.: 32 AF XY: 0.105 AC XY: 7836 AN XY: 74340

African (AFR) AF: 0.0268 AC: 1110 AN: 41456

American (AMR) AF: 0.183 AC: 2788 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0533 AC: 185 AN: 3470

East Asian (EAS) AF: 0.150 AC: 778 AN: 5180

South Asian (SAS) AF: 0.208 AC: 1002 AN: 4814

European-Finnish (FIN) AF: 0.0649 AC: 686 AN: 10574

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8822 AN: 67998

Other (OTH) AF: 0.0944 AC: 199 AN: 2108

Alfa AF: 0.121 Hom.: 2138

Bravo AF: 0.105

Asia WGS AF: 0.173 AC: 604 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.60
DANN	Benign	0.32
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs10484347; hg19: chr6-14013760;