rs4902642

Variant names:

• chr14-68743482-G-A
• rs4902642
• ENST00000768252.1:n.262-895C>T

Variant summary

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

The ENST00000768252.1(ENSG00000289583):​n.262-895C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 151,950 control chromosomes in the GnomAD database, including 10,933 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 0.37 (10933 hom., cov: 31)
• Consequence: ENSG00000289583 ENST00000768252.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.493
• Publications: 34 publications found

Genes affected

ENSG00000289583 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.417 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
ENSG00000289583	ENST00000768252.1	n.262-895C>T		intron_variant	Intron 2 of 3
ENSG00000289583	ENST00000768253.1	n.371-1339C>T		intron_variant	Intron 3 of 3
ENSG00000289583	ENST00000768254.1	n.234-895C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56286 AN: 151832 Hom.: 10924 Cov.: 31

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.371 AC: 56318 AN: 151950 Hom.: 10933 Cov.: 31 AF XY: 0.374 AC XY: 27758 AN XY: 74272

African (AFR) AF: 0.272 AC: 11270 AN: 41420

American (AMR) AF: 0.324 AC: 4953 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1389 AN: 3470

East Asian (EAS) AF: 0.299 AC: 1544 AN: 5170

South Asian (SAS) AF: 0.384 AC: 1852 AN: 4820

European-Finnish (FIN) AF: 0.537 AC: 5659 AN: 10540

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28593 AN: 67940

Other (OTH) AF: 0.369 AC: 776 AN: 2104

Alfa AF: 0.400 Hom.: 58182

Bravo AF: 0.348

Asia WGS AF: 0.388 AC: 1348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	9.3
DANN	Benign	0.77
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs4902642; hg19: chr14-69210199;