chr11-13074927-A-T

Variant names:

• chr11-13074927-A-T
• rs10500770
• ENST00000531136.1:n.48-19893T>A

Variant summary

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

The ENST00000531136.1(ENSG00000255558):​n.48-19893T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 151,984 control chromosomes in the GnomAD database, including 7,079 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 0.29 (7079 hom., cov: 32)
• Consequence: ENSG00000255558 ENST00000531136.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.284
• Publications: 4 publications found

Genes affected

ENSG00000255558 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000255558	ENST00000531136.1	n.48-19893T>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44757 AN: 151866 Hom.: 7074 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.0573

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.295 AC: 44782 AN: 151984 Hom.: 7079 Cov.: 32 AF XY: 0.289 AC XY: 21485 AN XY: 74280

African (AFR) AF: 0.220 AC: 9109 AN: 41446

American (AMR) AF: 0.336 AC: 5121 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1128 AN: 3472

East Asian (EAS) AF: 0.0574 AC: 297 AN: 5170

South Asian (SAS) AF: 0.273 AC: 1312 AN: 4808

European-Finnish (FIN) AF: 0.283 AC: 2988 AN: 10552

Middle Eastern (MID) AF: 0.390 AC: 114 AN: 292

European-Non Finnish (NFE) AF: 0.346 AC: 23527 AN: 67962

Other (OTH) AF: 0.313 AC: 662 AN: 2112

Alfa AF: 0.307 Hom.: 935

Bravo AF: 0.299

Asia WGS AF: 0.163 AC: 565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.4
DANN	Benign	0.44
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs10500770; hg19: chr11-13096474;