rs4697041

chr4-23601755-G-Achr4-23601755-G-Cchr4-23601755-G-T

Variant summary

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

The ENST00000514290.1(ENSG00000250137):n.117+40716G>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 0.43 in 151,110 control chromosomes in the GnomAD database, including 14,171 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 0.43 (14171 hom., cov: 30)
• Consequence: ENST00000514290.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.691

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000514290.1	n.117+40716G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.430 AC: 64855 AN: 151000 Hom.: 14142 Cov.: 30

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.430 AC: 64939 AN: 151110 Hom.: 14171 Cov.: 30 AF XY: 0.434 AC XY: 31964 AN XY: 73724

Gnomad4 AFR AF: 0.503

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.499

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.432

Alfa AF: 0.392 Hom.: 8978

Bravo AF: 0.428

Asia WGS AF: 0.477 AC: 1663 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	0.36
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4697041; hg19: chr4-23603378;