9-122115903-C-T

Variant names:

• chr9-122115903-C-T
• rs10985535
• ENST00000778328.1:n.601-4020C>T

Variant summary

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

The ENST00000778328.1(ENSG00000301342):​n.601-4020C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0764 in 152,206 control chromosomes in the GnomAD database, including 548 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 0.076 (548 hom., cov: 33)
• Consequence: ENSG00000301342 ENST00000778328.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 3 publications found

Genes affected

ENSG00000301342 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.218 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
ENSG00000301342	ENST00000778328.1	n.601-4020C>T		intron_variant	Intron 2 of 3
ENSG00000301342	ENST00000778332.1	n.218+135C>T		intron_variant	Intron 1 of 1
ENSG00000301342	ENST00000778333.1	n.105+135C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0764 AC: 11620 AN: 152088 Hom.: 546 Cov.: 33

Gnomad AFR AF: 0.0710

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.0817

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.0696

Gnomad FIN AF: 0.0748

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0668

Gnomad OTH AF: 0.0732

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

GnomAD4 genome AF: 0.0764 AC: 11627 AN: 152206 Hom.: 548 Cov.: 33 AF XY: 0.0778 AC XY: 5788 AN XY: 74414

African (AFR) AF: 0.0709 AC: 2947 AN: 41540

American (AMR) AF: 0.0818 AC: 1252 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 350 AN: 3472

East Asian (EAS) AF: 0.229 AC: 1177 AN: 5144

South Asian (SAS) AF: 0.0696 AC: 336 AN: 4826

European-Finnish (FIN) AF: 0.0748 AC: 793 AN: 10606

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0668 AC: 4543 AN: 67998

Other (OTH) AF: 0.0734 AC: 155 AN: 2112

Alfa AF: 0.0528 Hom.: 66

Bravo AF: 0.0776

Asia WGS AF: 0.145 AC: 504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	4.5
DANN	Benign	0.88
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs10985535; hg19: chr9-124878182;