rs735914

Variant names:

• chr9-79201386-C-T
• rs735914
• ENST00000722324.1:n.494C>T

Variant summary

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

The ENST00000722324.1(ENSG00000294269):​n.494C>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 0.579 in 152,010 control chromosomes in the GnomAD database, including 26,167 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 0.58 (26167 hom., cov: 32)
• Consequence: ENSG00000294269 ENST00000722324.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.120
• Publications: 4 publications found

Genes affected

ENSG00000294269 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902186	XR_007061599.1	n.180C>T		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294269	ENST00000722324.1	n.494C>T		non_coding_transcript_exon_variant	Exon 2 of 3
ENSG00000294269	ENST00000722325.1	n.487C>T		non_coding_transcript_exon_variant	Exon 2 of 3
ENSG00000294269	ENST00000722326.1	n.402C>T		non_coding_transcript_exon_variant	Exon 2 of 3

Frequencies

GnomAD3 genomes AF: 0.579 AC: 87926 AN: 151892 Hom.: 26140 Cov.: 32

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.579 AC: 88004 AN: 152010 Hom.: 26167 Cov.: 32 AF XY: 0.578 AC XY: 42925 AN XY: 74298

African (AFR) AF: 0.710 AC: 29454 AN: 41482

American (AMR) AF: 0.641 AC: 9777 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.599 AC: 2080 AN: 3470

East Asian (EAS) AF: 0.594 AC: 3060 AN: 5152

South Asian (SAS) AF: 0.380 AC: 1832 AN: 4818

European-Finnish (FIN) AF: 0.535 AC: 5661 AN: 10580

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.503 AC: 34193 AN: 67930

Other (OTH) AF: 0.604 AC: 1275 AN: 2112

Alfa AF: 0.551 Hom.: 9210

Bravo AF: 0.595

Asia WGS AF: 0.488 AC: 1701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.39
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs735914; hg19: chr9-81816301;