rs744511

Variant names:

• chr14-39627781-A-G
• rs744511
• ENST00000650911.1:n.113-27723A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000650911.1(ENSG00000258526):​n.113-27723A>G variant causes a intron 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: ENSG00000258526 ENST00000650911.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.746
• Publications: 7 publications found

Genes affected

ENSG00000258526 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105370461	XR_001750719.2	n.148-27064A>G		intron_variant	Intron 2 of 4
LOC105370461	XR_001750723.2	n.167-27064A>G		intron_variant	Intron 2 of 4
LOC105370461	XR_001750725.1	n.165-27064A>G		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258526	ENST00000650911.1	n.113-27723A>G		intron_variant	Intron 2 of 5
ENSG00000258526	ENST00000651829.1	n.641-14932A>G		intron_variant	Intron 6 of 13
ENSG00000258526	ENST00000652126.1	n.153-27723A>G		intron_variant	Intron 2 of 7

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

African (AFR) AF: 0.613 AC: 25409 AN: 41464

American (AMR) AF: 0.350 AC: 5340 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 743 AN: 3470

East Asian (EAS) AF: 0.453 AC: 2336 AN: 5160

South Asian (SAS) AF: 0.493 AC: 2376 AN: 4824

European-Finnish (FIN) AF: 0.386 AC: 4079 AN: 10562

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21917 AN: 67966

Other (OTH) AF: 0.365 AC: 768 AN: 2102

Alfa AF: 0.347 Hom.: 42009

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
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs744511; hg19: chr14-40096985;