9-73430347-T-C

Variant names:

• chr9-73430347-T-C
• rs1390948
• ENST00000715870.1:n.569A>G

Variant summary

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

The ENST00000715870.1(ENSG00000293609):​n.569A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 151,904 control chromosomes in the GnomAD database, including 2,157 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 0.10 (2157 hom., cov: 32)
• Consequence: ENSG00000293609 ENST00000715870.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29
• Publications: 1 publications found

Genes affected

ENSG00000293609 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715870.1. 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
	ENSG00000293609	ENST00000715870.1		n.569A>G		non_coding_transcript_exon	Exon 1 of 7
	ENSG00000293608	ENST00000715869.1		n.475+1189T>C		intron	N/A
	ENSG00000293608	ENST00000726719.1		n.1304+1189T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15458 AN: 151786 Hom.: 2158 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0540

Gnomad ASJ AF: 0.0133

Gnomad EAS AF: 0.0262

Gnomad SAS AF: 0.0346

Gnomad FIN AF: 0.00330

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0149

Gnomad OTH AF: 0.0781

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

GnomAD4 genome AF: 0.102 AC: 15472 AN: 151904 Hom.: 2157 Cov.: 32 AF XY: 0.0982 AC XY: 7295 AN XY: 74280

African (AFR) AF: 0.316 AC: 13066 AN: 41356

American (AMR) AF: 0.0540 AC: 822 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.0133 AC: 46 AN: 3464

East Asian (EAS) AF: 0.0253 AC: 130 AN: 5142

South Asian (SAS) AF: 0.0345 AC: 166 AN: 4816

European-Finnish (FIN) AF: 0.00330 AC: 35 AN: 10596

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0149 AC: 1013 AN: 67980

Other (OTH) AF: 0.0778 AC: 164 AN: 2108

Alfa AF: 0.0224 Hom.: 46

Bravo AF: 0.116

Asia WGS AF: 0.0630 AC: 220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.32
DANN	Benign	0.40
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs1390948; hg19: chr9-76045263;