9-117763702-C-G

Variant names:

• chr9-117763702-C-G
• rs10983777
• ENST00000697666.1:c.140+54973C>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000697666.1(ENSG00000285082):​c.140+54973C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,196 control chromosomes in the GnomAD database, including 1,727 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 0.13 (1727 hom., cov: 32)
• Consequence: ENSG00000285082 ENST00000697666.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00
• Publications: 3 publications found

Genes affected

ENSG00000285082 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000697666.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285082	ENST00000697666.1		c.140+54973C>G		intron	N/A	ENSP00000513391.1
	ENSG00000284977	ENST00000697672.1		n.4C>G		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000285082	ENST00000646089.2		c.93+59137C>G		intron	N/A	ENSP00000496197.1

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20517 AN: 152078 Hom.: 1727 Cov.: 32

Gnomad AFR AF: 0.0583

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.135 AC: 20516 AN: 152196 Hom.: 1727 Cov.: 32 AF XY: 0.134 AC XY: 9954 AN XY: 74388

African (AFR) AF: 0.0581 AC: 2416 AN: 41548

American (AMR) AF: 0.108 AC: 1650 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 387 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5176

South Asian (SAS) AF: 0.112 AC: 537 AN: 4812

European-Finnish (FIN) AF: 0.178 AC: 1887 AN: 10600

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13035 AN: 67990

Other (OTH) AF: 0.137 AC: 289 AN: 2114

Alfa AF: 0.160 Hom.: 263

Bravo AF: 0.127

Asia WGS AF: 0.0650 AC: 227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	12
DANN	Benign	0.65
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs10983777; hg19: chr9-120525980; COSMIC: COSV60396950;