9-117907005-A-C

Position:

• chr9-117907005-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000697639.1(ENSG00000284977):​n.1053+58850A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 151,984 control chromosomes in the GnomAD database, including 3,289 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 0.20 (3289 hom., cov: 32)
• Consequence: ENST00000697639.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.534

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000697639.1	n.1053+58850A>C		intron_variant, non_coding_transcript_variant
	ENST00000697724.1	n.1172+145556A>C		intron_variant, non_coding_transcript_variant
	ENST00000703416.1	n.346+58850A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30285 AN: 151866 Hom.: 3288 Cov.: 32

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.199 AC: 30311 AN: 151984 Hom.: 3289 Cov.: 32 AF XY: 0.196 AC XY: 14591 AN XY: 74266

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.221

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.202

Alfa AF: 0.180 Hom.: 382

Bravo AF: 0.205

Asia WGS AF: 0.237 AC: 823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.85
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1930706; hg19: chr9-120669283; COSMIC: COSV60397010;