rs1390948

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr9-73430347-T-C
• chr9-73430347-T-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376083	XR_001746729.1	n.569A>G		non_coding_transcript_exon_variant	Exon 1 of 7
LOC105376084	XR_007061581.1	n.349+1189T>C		intron_variant	Intron 3 of 6
LOC105376084	XR_929939.1	n.329+1189T>C		intron_variant	Intron 3 of 4
LOC105376084	XR_929941.2	n.349+1189T>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293609	ENST00000715870.1	n.569A>G		non_coding_transcript_exon_variant	Exon 1 of 7
ENSG00000293608	ENST00000715869.1	n.475+1189T>C		intron_variant	Intron 4 of 4
ENSG00000293608	ENST00000726719.1	n.1304+1189T>C		intron_variant	Intron 11 of 12

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 v4.3

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;