rs1016013

Variant names:

• chr9-94714202-A-G
• rs1016013
• ENST00000724122.1:n.232+3515T>C

Your query was ambiguous. Multiple possible variants found:

• chr9-94714202-A-G
• chr9-94714202-A-T

Variant summary

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

The ENST00000724122.1(ENSG00000294530):​n.232+3515T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.67 in 152,054 control chromosomes in the GnomAD database, including 34,777 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 0.67 (34777 hom., cov: 32)
• Consequence: ENSG00000294530 ENST00000724122.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.30
• Publications: 10 publications found

Genes affected

ENSG00000294530 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.801 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
ENSG00000294530	ENST00000724122.1	n.232+3515T>C		intron_variant	Intron 2 of 3
ENSG00000294530	ENST00000724123.1	n.226+3515T>C		intron_variant	Intron 2 of 4
ENSG00000294530	ENST00000724124.1	n.210+3515T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.670 AC: 101771 AN: 151936 Hom.: 34732 Cov.: 32

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.670 AC: 101874 AN: 152054 Hom.: 34777 Cov.: 32 AF XY: 0.674 AC XY: 50141 AN XY: 74338

African (AFR) AF: 0.790 AC: 32781 AN: 41490

American (AMR) AF: 0.690 AC: 10533 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1866 AN: 3468

East Asian (EAS) AF: 0.822 AC: 4242 AN: 5160

South Asian (SAS) AF: 0.748 AC: 3598 AN: 4808

European-Finnish (FIN) AF: 0.650 AC: 6878 AN: 10574

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.586 AC: 39820 AN: 67964

Other (OTH) AF: 0.645 AC: 1362 AN: 2112

Alfa AF: 0.595 Hom.: 12512

Bravo AF: 0.678

Asia WGS AF: 0.805 AC: 2802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.019
DANN	Benign	0.25
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs1016013; hg19: chr9-97476484;