rs10484555

Variant names:

• chr6-31313688-T-C
• rs10484555

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 0.0193 in 145,666 control chromosomes in the GnomAD database, including 357 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 0.019 (357 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0633 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: 0.0193 AC: 2802 AN: 145552 Hom.: 357 Cov.: 29

Gnomad AFR AF: 0.0507

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00651

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0697

Gnomad SAS AF: 0.0668

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000621

Gnomad OTH AF: 0.0138

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

GnomAD4 genome AF: 0.0193 AC: 2806 AN: 145666 Hom.: 357 Cov.: 29 AF XY: 0.0208 AC XY: 1476 AN XY: 71018

Gnomad4 AFR AF: 0.0507

Gnomad4 AMR AF: 0.00650

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.0694

Gnomad4 SAS AF: 0.0663

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000621

Gnomad4 OTH AF: 0.0152

Alfa AF: 0.0146 Hom.: 22

Asia WGS AF: 0.0880 AC: 297 AN: 3372

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484555; hg19: chr6-31281465;