rs7540934

Variant names:

• chr1-109941151-G-A
• rs7540934
• ENST00000746854.1:n.718C>T

Variant summary

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

The ENST00000746854.1(ENSG00000297293):​n.718C>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 0.379 in 151,924 control chromosomes in the GnomAD database, including 11,266 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 0.38 (11266 hom., cov: 31)
• Consequence: ENSG00000297293 ENST00000746854.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270
• Publications: 7 publications found

Genes affected

ENSG00000297293 (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 (NFE) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000746854.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297293	ENST00000746854.1		n.718C>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57483 AN: 151806 Hom.: 11258 Cov.: 31

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.0584

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.379 AC: 57506 AN: 151924 Hom.: 11266 Cov.: 31 AF XY: 0.376 AC XY: 27894 AN XY: 74226

African (AFR) AF: 0.366 AC: 15136 AN: 41400

American (AMR) AF: 0.347 AC: 5296 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1421 AN: 3470

East Asian (EAS) AF: 0.0587 AC: 304 AN: 5180

South Asian (SAS) AF: 0.275 AC: 1324 AN: 4818

European-Finnish (FIN) AF: 0.459 AC: 4829 AN: 10522

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.412 AC: 27979 AN: 67946

Other (OTH) AF: 0.391 AC: 825 AN: 2112

Alfa AF: 0.396 Hom.: 42007

Bravo AF: 0.369

Asia WGS AF: 0.181 AC: 631 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	7.6
DANN	Benign	0.58
PhyloP100		0.027

Splicing

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

Other links and lift over

dbSNP: rs7540934; hg19: chr1-110483773;