rs6482235

Variant names:

• chr10-22734037-T-C
• rs6482235

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 0.397 in 151,818 control chromosomes in the GnomAD database, including 14,121 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 0.40 (14121 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.647 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: 0.397 AC: 60163 AN: 151700 Hom.: 14079 Cov.: 31

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.397 AC: 60249 AN: 151818 Hom.: 14121 Cov.: 31 AF XY: 0.389 AC XY: 28862 AN XY: 74170

Gnomad4 AFR AF: 0.654

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.395

Alfa AF: 0.331 Hom.: 12551

Bravo AF: 0.406

Asia WGS AF: 0.272 AC: 948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.63
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6482235; hg19: chr10-23022966;