rs7702514

Variant names:

• chr5-87431210-C-T
• rs7702514
• ENST00000644559.1:n.720+18149C>T

Variant summary

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

The ENST00000644559.1(ENSG00000285190):​n.720+18149C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,136 control chromosomes in the GnomAD database, including 1,374 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 0.12 (1374 hom., cov: 31)
• Consequence: ENSG00000285190 ENST00000644559.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205
• Publications: 10 publications found

Genes affected

ENSG00000285190 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379066	XR_948542.2	n.78-1414C>T		intron_variant	Intron 1 of 3
LOC105379066	XR_948543.1	n.80+18149C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285190	ENST00000644559.1	n.720+18149C>T		intron_variant	Intron 1 of 4
ENSG00000285190	ENST00000797782.1	n.684+18149C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17925 AN: 152018 Hom.: 1375 Cov.: 31

Gnomad AFR AF: 0.0315

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.0986

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.0398

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.118 AC: 17924 AN: 152136 Hom.: 1374 Cov.: 31 AF XY: 0.118 AC XY: 8751 AN XY: 74376

African (AFR) AF: 0.0314 AC: 1305 AN: 41526

American (AMR) AF: 0.0984 AC: 1503 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 598 AN: 3468

East Asian (EAS) AF: 0.0400 AC: 207 AN: 5170

South Asian (SAS) AF: 0.249 AC: 1200 AN: 4814

European-Finnish (FIN) AF: 0.111 AC: 1176 AN: 10590

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11426 AN: 67976

Other (OTH) AF: 0.118 AC: 249 AN: 2108

Alfa AF: 0.155 Hom.: 3992

Bravo AF: 0.113

Asia WGS AF: 0.139 AC: 485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.24
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs7702514; hg19: chr5-86727027;