rs10484676

Variant names:

• chr6-147983562-T-C
• rs10484676

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 0.088 in 152,288 control chromosomes in the GnomAD database, including 607 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 0.088 (607 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.107 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: 0.0880 AC: 13392 AN: 152170 Hom.: 608 Cov.: 33

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.0570

Gnomad ASJ AF: 0.0381

Gnomad EAS AF: 0.0113

Gnomad SAS AF: 0.0128

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0931

Gnomad OTH AF: 0.0765

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

GnomAD4 genome AF: 0.0880 AC: 13405 AN: 152288 Hom.: 607 Cov.: 33 AF XY: 0.0861 AC XY: 6414 AN XY: 74468

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.0570

Gnomad4 ASJ AF: 0.0381

Gnomad4 EAS AF: 0.0112

Gnomad4 SAS AF: 0.0130

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.0931

Gnomad4 OTH AF: 0.0757

Alfa AF: 0.0880 Hom.: 290

Bravo AF: 0.0865

Asia WGS AF: 0.0260 AC: 90 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.15
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484676; hg19: chr6-148304698;