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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000722324.1. 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
	ENSG00000294269	ENST00000722324.1		n.494C>T		non_coding_transcript_exon	Exon 2 of 3
	ENSG00000294269	ENST00000722325.1		n.487C>T		non_coding_transcript_exon	Exon 2 of 3
	ENSG00000294269	ENST00000722326.1		n.402C>T		non_coding_transcript_exon	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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs735914;

hg19: chr9-81816301;