rs749514

Variant names:

• chr11-127485946-G-A
• rs749514
• ENST00000822754.1:n.233-8344G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-127485946-G-A
• chr11-127485946-G-T

Variant summary

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

The ENST00000822754.1(ENSG00000307024):​n.233-8344G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 151,968 control chromosomes in the GnomAD database, including 5,806 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 0.26 (5806 hom., cov: 31)
• Consequence: ENSG00000307024 ENST00000822754.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.619
• Publications: 3 publications found

Genes affected

ENSG00000307024 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984373	XR_001748081.2	n.128-8344G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307024	ENST00000822754.1	n.233-8344G>A		intron_variant	Intron 2 of 3
ENSG00000307024	ENST00000822755.1	n.270-10216G>A		intron_variant	Intron 2 of 2
ENSG00000307024	ENST00000822756.1	n.224-10216G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38914 AN: 151850 Hom.: 5805 Cov.: 31

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.256 AC: 38924 AN: 151968 Hom.: 5806 Cov.: 31 AF XY: 0.258 AC XY: 19159 AN XY: 74292

African (AFR) AF: 0.108 AC: 4486 AN: 41472

American (AMR) AF: 0.319 AC: 4872 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1007 AN: 3462

East Asian (EAS) AF: 0.444 AC: 2288 AN: 5156

South Asian (SAS) AF: 0.203 AC: 975 AN: 4814

European-Finnish (FIN) AF: 0.296 AC: 3124 AN: 10548

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.311 AC: 21112 AN: 67946

Other (OTH) AF: 0.290 AC: 610 AN: 2106

Alfa AF: 0.173 Hom.: 546

Bravo AF: 0.254

Asia WGS AF: 0.261 AC: 908 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.15
DANN	Benign	0.64
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs749514; hg19: chr11-127355841;