9-85503122-C-T

Variant names:

• chr9-85503122-C-T
• rs2378688
• ENST00000812125.1:n.138+13208G>A

Variant summary

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

The ENST00000812125.1(ENSG00000285634):​n.138+13208G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 152,056 control chromosomes in the GnomAD database, including 25,859 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 0.58 (25859 hom., cov: 32)
• Consequence: ENSG00000285634 ENST00000812125.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250
• Publications: 6 publications found

Genes affected

ENSG00000285634 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.62 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
ENSG00000285634	ENST00000812125.1	n.138+13208G>A		intron_variant	Intron 2 of 4
ENSG00000285634	ENST00000812126.1	n.153+13208G>A		intron_variant	Intron 1 of 4
ENSG00000285634	ENST00000812127.1	n.123+7916G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88339 AN: 151938 Hom.: 25841 Cov.: 32

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.581 AC: 88394 AN: 152056 Hom.: 25859 Cov.: 32 AF XY: 0.579 AC XY: 43022 AN XY: 74336

African (AFR) AF: 0.626 AC: 25973 AN: 41466

American (AMR) AF: 0.530 AC: 8102 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2112 AN: 3472

East Asian (EAS) AF: 0.611 AC: 3153 AN: 5160

South Asian (SAS) AF: 0.605 AC: 2911 AN: 4814

European-Finnish (FIN) AF: 0.521 AC: 5516 AN: 10578

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.572 AC: 38848 AN: 67966

Other (OTH) AF: 0.584 AC: 1234 AN: 2112

Alfa AF: 0.586 Hom.: 60939

Bravo AF: 0.585

Asia WGS AF: 0.589 AC: 2049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.40
PhyloP100		-0.025

Splicing

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

Other links and lift over

dbSNP: rs2378688; hg19: chr9-88118037;