rs10501483

Variant names:

• chr11-80894035-T-G
• rs10501483
• ENST00000795280.1:n.79+18256A>C

Variant summary

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

The ENST00000795280.1(ENSG00000303527):​n.79+18256A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0866 in 152,216 control chromosomes in the GnomAD database, including 1,731 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 0.087 (1731 hom., cov: 31)
• Consequence: ENSG00000303527 ENST00000795280.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 2 publications found

Genes affected

ENSG00000303527 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.28 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
ENSG00000303527	ENST00000795280.1	n.79+18256A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0866 AC: 13169 AN: 152098 Hom.: 1727 Cov.: 31

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0411

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.0270

Gnomad SAS AF: 0.00684

Gnomad FIN AF: 0.0137

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.00326

Gnomad OTH AF: 0.0764

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

GnomAD4 genome AF: 0.0866 AC: 13187 AN: 152216 Hom.: 1731 Cov.: 31 AF XY: 0.0847 AC XY: 6305 AN XY: 74438

African (AFR) AF: 0.284 AC: 11785 AN: 41482

American (AMR) AF: 0.0410 AC: 627 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0173 AC: 60 AN: 3472

East Asian (EAS) AF: 0.0269 AC: 139 AN: 5176

South Asian (SAS) AF: 0.00684 AC: 33 AN: 4824

European-Finnish (FIN) AF: 0.0137 AC: 146 AN: 10626

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.00325 AC: 221 AN: 68020

Other (OTH) AF: 0.0756 AC: 160 AN: 2116

Alfa AF: 0.0455 Hom.: 307

Bravo AF: 0.0975

Asia WGS AF: 0.0400 AC: 138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	11
DANN	Benign	0.46
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs10501483; hg19: chr11-80605078;