9-2696555-G-A

Variant names:

• chr9-2696555-G-A
• rs930811
• ENST00000768783.1:n.114-28494C>T

Variant summary

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

The ENST00000768783.1(ENSG00000286670):​n.114-28494C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 151,992 control chromosomes in the GnomAD database, including 17,502 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 0.47 (17502 hom., cov: 33)
• Consequence: ENSG00000286670 ENST00000768783.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 5 publications found

Genes affected

ENSG00000286670 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.688 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
ENSG00000286670	ENST00000768783.1	n.114-28494C>T		intron_variant	Intron 1 of 3
ENSG00000286670	ENST00000768784.1	n.157-28494C>T		intron_variant	Intron 1 of 3
ENSG00000286670	ENST00000768785.1	n.157-31480C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71896 AN: 151874 Hom.: 17474 Cov.: 33

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.473 AC: 71959 AN: 151992 Hom.: 17502 Cov.: 33 AF XY: 0.477 AC XY: 35460 AN XY: 74304

African (AFR) AF: 0.521 AC: 21583 AN: 41440

American (AMR) AF: 0.531 AC: 8118 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1495 AN: 3472

East Asian (EAS) AF: 0.708 AC: 3655 AN: 5166

South Asian (SAS) AF: 0.499 AC: 2404 AN: 4820

European-Finnish (FIN) AF: 0.428 AC: 4510 AN: 10540

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28585 AN: 67958

Other (OTH) AF: 0.480 AC: 1012 AN: 2110

Alfa AF: 0.442 Hom.: 62621

Bravo AF: 0.484

Asia WGS AF: 0.609 AC: 2115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0070
DANN	Benign	0.55
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs930811; hg19: chr9-2696555;