rs1342022

Variant names:

• chr9-73090591-G-A
• rs1342022
• ENST00000715863.1:n.1782C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-73090591-G-A
• chr9-73090591-G-T

Variant summary

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

The ENST00000715863.1(ENSG00000293607):​n.1782C>T 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 0.573 in 151,862 control chromosomes in the GnomAD database, including 26,992 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 0.57 (26992 hom., cov: 32)
• Consequence: ENSG00000293607 ENST00000715863.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.295
• Publications: 6 publications found

Genes affected

ENSG00000293607 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376081	XR_929926.2	n.1813C>T		non_coding_transcript_exon_variant	Exon 4 of 4
LOC105376081	XR_929927.2	n.1750C>T		non_coding_transcript_exon_variant	Exon 4 of 4
LOC105376081	XR_929928.2	n.1622C>T		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293607	ENST00000715863.1	n.1782C>T		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000293607	ENST00000719114.1	n.1726C>T		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000293607	ENST00000719115.1	n.1653C>T		non_coding_transcript_exon_variant	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.573 AC: 86906 AN: 151744 Hom.: 26980 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.573 AC: 86965 AN: 151862 Hom.: 26992 Cov.: 32 AF XY: 0.578 AC XY: 42903 AN XY: 74208

African (AFR) AF: 0.317 AC: 13115 AN: 41392

American (AMR) AF: 0.638 AC: 9735 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2143 AN: 3470

East Asian (EAS) AF: 0.455 AC: 2347 AN: 5158

South Asian (SAS) AF: 0.658 AC: 3172 AN: 4820

European-Finnish (FIN) AF: 0.748 AC: 7893 AN: 10558

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.684 AC: 46425 AN: 67904

Other (OTH) AF: 0.614 AC: 1291 AN: 2104

Alfa AF: 0.637 Hom.: 16075

Bravo AF: 0.550

Asia WGS AF: 0.547 AC: 1900 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.46
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs1342022; hg19: chr9-75705507;