rs6482235

Variant names:

• chr10-22734037-T-C
• rs6482235
• ENST00000756996.1:n.497-992A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000756996.1(ENSG00000298626):​n.497-992A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000298626 ENST00000756996.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 4 publications found

Genes affected

ENSG00000298626 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000298626	ENST00000756996.1	n.497-992A>G		intron_variant	Intron 3 of 3

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

African (AFR) AF: 0.654 AC: 27039 AN: 41344

American (AMR) AF: 0.264 AC: 4028 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1246 AN: 3470

East Asian (EAS) AF: 0.105 AC: 542 AN: 5172

South Asian (SAS) AF: 0.368 AC: 1768 AN: 4808

European-Finnish (FIN) AF: 0.256 AC: 2685 AN: 10498

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21755 AN: 67956

Other (OTH) AF: 0.395 AC: 832 AN: 2106

Alfa AF: 0.340 Hom.: 18326

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
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs6482235; hg19: chr10-23022966;