rs10738147

Variant names:

• chr9-1012154-T-C
• rs10738147
• ENST00000823816.1:n.412-6013T>C

Your query was ambiguous. Multiple possible variants found:

• chr9-1012154-T-C
• chr9-1012154-T-G

Variant summary

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

The ENST00000823816.1(ENSG00000307091):​n.412-6013T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 152,116 control chromosomes in the GnomAD database, including 32,434 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 0.64 (32434 hom., cov: 33)
• Consequence: ENSG00000307091 ENST00000823816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.421
• Publications: 3 publications found

Genes affected

ENSG00000307091 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.798 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
ENSG00000307091	ENST00000823816.1	n.412-6013T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97701 AN: 151998 Hom.: 32393 Cov.: 33

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.643 AC: 97803 AN: 152116 Hom.: 32434 Cov.: 33 AF XY: 0.642 AC XY: 47746 AN XY: 74350

African (AFR) AF: 0.805 AC: 33432 AN: 41516

American (AMR) AF: 0.514 AC: 7852 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1646 AN: 3472

East Asian (EAS) AF: 0.609 AC: 3144 AN: 5164

South Asian (SAS) AF: 0.419 AC: 2018 AN: 4818

European-Finnish (FIN) AF: 0.672 AC: 7095 AN: 10554

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.599 AC: 40721 AN: 67988

Other (OTH) AF: 0.589 AC: 1243 AN: 2112

Alfa AF: 0.605 Hom.: 78994

Bravo AF: 0.642

Asia WGS AF: 0.492 AC: 1716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.1
DANN	Benign	0.38
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs10738147; hg19: chr9-1012154;