rs744511

Positions:

• chr14-39627781-A-G
• chr14-39627781-A-T

Variant summary

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

The ENST00000652126.1(ENSG00000258526):​n.153-27723A>G 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 0.416 in 152,020 control chromosomes in the GnomAD database, including 14,528 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 0.42 (14528 hom., cov: 32)
• Consequence: ENST00000652126.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.746

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370461	XR_001750723.2	n.167-27064A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000652126.1	n.153-27723A>G		intron_variant, non_coding_transcript_variant
	ENST00000650911.1	n.113-27723A>G		intron_variant, non_coding_transcript_variant
	ENST00000651829.1	n.641-14932A>G		intron_variant, non_coding_transcript_variant
	ENST00000662828.1	n.115-27723A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63232 AN: 151902 Hom.: 14512 Cov.: 32

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.416 AC: 63299 AN: 152020 Hom.: 14528 Cov.: 32 AF XY: 0.418 AC XY: 31090 AN XY: 74318

Gnomad4 AFR AF: 0.613

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.214

Gnomad4 EAS AF: 0.453

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.365

Alfa AF: 0.331 Hom.: 17733

Bravo AF: 0.416

Asia WGS AF: 0.510 AC: 1776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.4
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs744511; hg19: chr14-40096985;