rs4702982

Variant names:

• chr5-100655944-C-T
• rs4702982
• ENST00000511592.1:n.153-469G>A

Variant summary

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

The ENST00000511592.1(ENSG00000250806):​n.153-469G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0904 in 152,046 control chromosomes in the GnomAD database, including 855 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 0.090 (855 hom., cov: 32)
• Consequence: ENSG00000250806 ENST00000511592.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750
• Publications: 17 publications found

Genes affected

ENSG00000250806 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.201 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
ENSG00000250806	ENST00000511592.1	n.153-469G>A		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.0903 AC: 13726 AN: 151928 Hom.: 853 Cov.: 32

Gnomad AFR AF: 0.0276

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.0612

Gnomad FIN AF: 0.0835

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0963

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.0904 AC: 13741 AN: 152046 Hom.: 855 Cov.: 32 AF XY: 0.0913 AC XY: 6783 AN XY: 74318

African (AFR) AF: 0.0276 AC: 1146 AN: 41478

American (AMR) AF: 0.202 AC: 3092 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 353 AN: 3470

East Asian (EAS) AF: 0.212 AC: 1093 AN: 5166

South Asian (SAS) AF: 0.0614 AC: 296 AN: 4818

European-Finnish (FIN) AF: 0.0835 AC: 882 AN: 10564

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0962 AC: 6542 AN: 67970

Other (OTH) AF: 0.105 AC: 220 AN: 2104

Alfa AF: 0.0984 Hom.: 1996

Bravo AF: 0.100

Asia WGS AF: 0.133 AC: 460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.4
DANN	Benign	0.40
PhyloP100		0.075
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs4702982; hg19: chr5-99991648;