rs1930713

Variant names:

• chr9-117971434-G-A
• rs1930713
• ENST00000665764.1:n.*17-665G>A

Variant summary

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

The ENST00000665764.1(ENSG00000285082):​n.*17-665G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 152,194 control chromosomes in the GnomAD database, including 4,217 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 0.23 (4217 hom., cov: 33)
• Consequence: ENSG00000285082 ENST00000665764.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.224

Genes affected

ENSG00000285082 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.244 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
ENSG00000285082	ENST00000665764.1	n.*17-665G>A		intron_variant	Intron 2 of 6			ENSP00000499745.1
ENSG00000285082	ENST00000697636.1	n.*17-85596G>A		intron_variant	Intron 2 of 5			ENSP00000513366.1
ENSG00000284977	ENST00000697639.1	n.1054-85596G>A		intron_variant	Intron 7 of 12

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34731 AN: 152076 Hom.: 4211 Cov.: 33

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.0384

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.228 AC: 34758 AN: 152194 Hom.: 4217 Cov.: 33 AF XY: 0.226 AC XY: 16789 AN XY: 74422

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.0383

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.246

Alfa AF: 0.245 Hom.: 9659

Bravo AF: 0.227

Asia WGS AF: 0.115 AC: 401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1930713; hg19: chr9-120733712;