rs7140723

Variant names:

• chr14-43636495-C-A
• rs7140723
• ENST00000807481.1:n.400+14716G>T

Variant summary

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

The ENST00000807481.1(ENSG00000304974):​n.400+14716G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,002 control chromosomes in the GnomAD database, including 1,074 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 0.11 (1074 hom., cov: 32)
• Consequence: ENSG00000304974 ENST00000807481.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.712
• Publications: 1 publications found

Genes affected

ENSG00000304974 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304974	ENST00000807481.1	n.400+14716G>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16867 AN: 151884 Hom.: 1075 Cov.: 32

Gnomad AFR AF: 0.0636

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.0815

Gnomad ASJ AF: 0.0934

Gnomad EAS AF: 0.0183

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.111 AC: 16872 AN: 152002 Hom.: 1074 Cov.: 32 AF XY: 0.109 AC XY: 8116 AN XY: 74290

African (AFR) AF: 0.0636 AC: 2638 AN: 41484

American (AMR) AF: 0.0815 AC: 1243 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0934 AC: 324 AN: 3468

East Asian (EAS) AF: 0.0184 AC: 95 AN: 5176

South Asian (SAS) AF: 0.137 AC: 660 AN: 4818

European-Finnish (FIN) AF: 0.151 AC: 1599 AN: 10572

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 9984 AN: 67910

Other (OTH) AF: 0.101 AC: 214 AN: 2112

Alfa AF: 0.129 Hom.: 1423

Bravo AF: 0.101

Asia WGS AF: 0.0670 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.35
DANN	Benign	0.28
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs7140723; hg19: chr14-44105698;