rs1514989

Positions:

• chr4-17040440-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000511735.1(ENSG00000249998):​n.154+20267G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 152,098 control chromosomes in the GnomAD database, including 20,156 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 0.50 (20156 hom., cov: 33)
• Consequence: ENST00000511735.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.340

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000511735.1	n.154+20267G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.500 AC: 75927 AN: 151980 Hom.: 20116 Cov.: 33

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.500 AC: 76023 AN: 152098 Hom.: 20156 Cov.: 33 AF XY: 0.500 AC XY: 37194 AN XY: 74366

Gnomad4 AFR AF: 0.687

Gnomad4 AMR AF: 0.419

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.573

Gnomad4 FIN AF: 0.437

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.483

Alfa AF: 0.443 Hom.: 13706

Bravo AF: 0.498

Asia WGS AF: 0.439 AC: 1527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.0
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1514989; hg19: chr4-17042063;