rs2983733

Variant names:

• chr14-64382697-G-A
• rs2983733
• ENST00000641479.1:n.570+4720C>T

Variant summary

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

The ENST00000641479.1(ENSG00000293482):​n.570+4720C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 152,184 control chromosomes in the GnomAD database, including 23,113 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 0.52 (23113 hom., cov: 34)
• Consequence: ENSG00000293482 ENST00000641479.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590
• Publications: 9 publications found

Genes affected

ENSG00000293482 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.801 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
ENSG00000293482	ENST00000641479.1	n.570+4720C>T		intron_variant	Intron 1 of 6
ENSG00000293482	ENST00000641725.1	n.465+3892C>T		intron_variant	Intron 1 of 5
ENSG00000293482	ENST00000771648.1	n.75+5515C>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78492 AN: 152066 Hom.: 23078 Cov.: 34

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.516 AC: 78582 AN: 152184 Hom.: 23113 Cov.: 34 AF XY: 0.505 AC XY: 37599 AN XY: 74394

African (AFR) AF: 0.808 AC: 33556 AN: 41536

American (AMR) AF: 0.402 AC: 6148 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.549 AC: 1905 AN: 3472

East Asian (EAS) AF: 0.152 AC: 787 AN: 5184

South Asian (SAS) AF: 0.417 AC: 2014 AN: 4826

European-Finnish (FIN) AF: 0.312 AC: 3307 AN: 10594

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29170 AN: 67972

Other (OTH) AF: 0.496 AC: 1047 AN: 2112

Alfa AF: 0.498 Hom.: 4613

Bravo AF: 0.532

Asia WGS AF: 0.322 AC: 1119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.29
DANN	Benign	0.17
PhyloP100		-0.059

Splicing

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

Other links and lift over

dbSNP: rs2983733; hg19: chr14-64849415;