rs10511884

Variant names:

• chr9-31678990-C-T
• rs10511884
• ENST00000804476.1:n.111-44744G>A

Variant summary

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

The ENST00000804476.1(ENSG00000304547):​n.111-44744G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 151,800 control chromosomes in the GnomAD database, including 3,714 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 0.22 (3714 hom., cov: 32)
• Consequence: ENSG00000304547 ENST00000804476.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290
• Publications: 4 publications found

Genes affected

ENSG00000304547 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.289 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
ENSG00000304547	ENST00000804476.1	n.111-44744G>A		intron_variant	Intron 1 of 2
ENSG00000304547	ENST00000804477.1	n.139+14247G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33449 AN: 151682 Hom.: 3701 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.221 AC: 33499 AN: 151800 Hom.: 3714 Cov.: 32 AF XY: 0.219 AC XY: 16280 AN XY: 74176

African (AFR) AF: 0.216 AC: 8950 AN: 41446

American (AMR) AF: 0.296 AC: 4492 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 781 AN: 3470

East Asian (EAS) AF: 0.135 AC: 694 AN: 5152

South Asian (SAS) AF: 0.132 AC: 635 AN: 4822

European-Finnish (FIN) AF: 0.211 AC: 2234 AN: 10568

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 15025 AN: 67852

Other (OTH) AF: 0.247 AC: 520 AN: 2108

Alfa AF: 0.222 Hom.: 7756

Bravo AF: 0.230

Asia WGS AF: 0.133 AC: 460 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.32
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs10511884; hg19: chr9-31678988;