rs1930713

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

ENSG00000285082 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000665764.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285082	ENST00000665764.1		n.*17-665G>A		intron	N/A	ENSP00000499745.1	A0A2R8YGN2
	ENSG00000285082	ENST00000697636.1		n.*17-85596G>A		intron	N/A	ENSP00000513366.1	A0A2R8YGN2
	ENSG00000284977	ENST00000697639.1		n.1054-85596G>A		intron	N/A

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

African (AFR) AF: 0.222 AC: 9229 AN: 41530

American (AMR) AF: 0.207 AC: 3173 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1328 AN: 3468

East Asian (EAS) AF: 0.0383 AC: 198 AN: 5176

South Asian (SAS) AF: 0.182 AC: 881 AN: 4828

European-Finnish (FIN) AF: 0.222 AC: 2355 AN: 10594

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16830 AN: 67986

Other (OTH) AF: 0.246 AC: 519 AN: 2114

Alfa AF: 0.242 Hom.: 19579

Bravo AF: 0.227

Asia WGS AF: 0.115 AC: 401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.58
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs1930713; hg19: chr9-120733712;