rs6482235

Positions:

• chr10-22734037-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;