ENST00000532770.2:n.146+703T>C

Variant names:

• chr11-92931709-T-C
• rs737383
• ENST00000532770.2:n.146+703T>C

Variant summary

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

The ENST00000532770.2(ENSG00000254874):​n.146+703T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 151,860 control chromosomes in the GnomAD database, including 22,446 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 0.53 (22446 hom., cov: 31)
• Consequence: ENSG00000254874 ENST00000532770.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.50
• Publications: 3 publications found

Genes affected

ENSG00000254874 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.7 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
ENSG00000254874	ENST00000532770.2	n.146+703T>C		intron_variant	Intron 1 of 3	2
ENSG00000254874	ENST00000749785.1	n.128+703T>C		intron_variant	Intron 1 of 2
ENSG00000254874	ENST00000749786.1	n.115+703T>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80066 AN: 151738 Hom.: 22387 Cov.: 31

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.528 AC: 80198 AN: 151860 Hom.: 22446 Cov.: 31 AF XY: 0.533 AC XY: 39539 AN XY: 74192

African (AFR) AF: 0.706 AC: 29266 AN: 41428

American (AMR) AF: 0.575 AC: 8782 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1409 AN: 3470

East Asian (EAS) AF: 0.618 AC: 3180 AN: 5142

South Asian (SAS) AF: 0.577 AC: 2767 AN: 4794

European-Finnish (FIN) AF: 0.463 AC: 4867 AN: 10512

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28440 AN: 67932

Other (OTH) AF: 0.519 AC: 1096 AN: 2112

Alfa AF: 0.465 Hom.: 31347

Bravo AF: 0.544

Asia WGS AF: 0.637 AC: 2214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.016
DANN	Benign	0.43
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs737383; hg19: chr11-92664875;