chr9-104529720-T-C

Variant names:

• chr9-104529720-T-C
• rs10761033
• ENST00000635678.1:n.348-6206T>C

Variant summary

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

The ENST00000635678.1(ENSG00000283001):​n.348-6206T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 151,848 control chromosomes in the GnomAD database, including 12,021 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 0.39 (12021 hom., cov: 31)
• Consequence: ENSG00000283001 ENST00000635678.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288
• Publications: 2 publications found

Genes affected

ENSG00000283001 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 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
ENSG00000283001	ENST00000635678.1	n.348-6206T>C		intron_variant	Intron 1 of 1	5
ENSG00000283001	ENST00000653242.1	n.299-6206T>C		intron_variant	Intron 1 of 2
ENSG00000283001	ENST00000658313.1	n.101-6206T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59112 AN: 151730 Hom.: 12007 Cov.: 31

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.390 AC: 59173 AN: 151848 Hom.: 12021 Cov.: 31 AF XY: 0.396 AC XY: 29413 AN XY: 74184

African (AFR) AF: 0.447 AC: 18513 AN: 41424

American (AMR) AF: 0.339 AC: 5157 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1118 AN: 3466

East Asian (EAS) AF: 0.725 AC: 3734 AN: 5150

South Asian (SAS) AF: 0.542 AC: 2608 AN: 4808

European-Finnish (FIN) AF: 0.395 AC: 4158 AN: 10532

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22642 AN: 67926

Other (OTH) AF: 0.389 AC: 821 AN: 2108

Alfa AF: 0.348 Hom.: 14864

Bravo AF: 0.387

Asia WGS AF: 0.619 AC: 2149 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.5
DANN	Benign	0.78
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs10761033; hg19: chr9-107292001;