rs1747856

Variant names:

• chr9-136141208-T-C
• rs1747856
• ENST00000813183.1:n.89+1037A>G

Variant summary

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

The ENST00000813183.1(ENSG00000305829):​n.89+1037A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,220 control chromosomes in the GnomAD database, including 1,822 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 0.11 (1822 hom., cov: 32)
• Consequence: ENSG00000305829 ENST00000813183.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.429
• Publications: 3 publications found

Genes affected

ENSG00000305829 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.281 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
ENSG00000305829	ENST00000813183.1	n.89+1037A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16374 AN: 152102 Hom.: 1813 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0582

Gnomad ASJ AF: 0.0603

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.0646

Gnomad FIN AF: 0.00565

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0422

Gnomad OTH AF: 0.0846

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

GnomAD4 genome AF: 0.108 AC: 16425 AN: 152220 Hom.: 1822 Cov.: 32 AF XY: 0.104 AC XY: 7708 AN XY: 74446

African (AFR) AF: 0.285 AC: 11821 AN: 41480

American (AMR) AF: 0.0581 AC: 889 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0603 AC: 209 AN: 3468

East Asian (EAS) AF: 0.00289 AC: 15 AN: 5184

South Asian (SAS) AF: 0.0642 AC: 310 AN: 4828

European-Finnish (FIN) AF: 0.00565 AC: 60 AN: 10614

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0422 AC: 2870 AN: 68018

Other (OTH) AF: 0.0837 AC: 177 AN: 2114

Alfa AF: 0.0783 Hom.: 1611

Bravo AF: 0.118

Asia WGS AF: 0.0510 AC: 177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.72
DANN	Benign	0.45
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs1747856; hg19: chr9-139033054;