ENST00000756757.1:n.234+27263C>T

Variant names:

• chr3-77995538-G-A
• rs9836484
• ENST00000756757.1:n.234+27263C>T

Variant summary

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

The ENST00000756757.1(ENSG00000298601):​n.234+27263C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 151,524 control chromosomes in the GnomAD database, including 8,900 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 0.34 (8900 hom., cov: 31)
• Consequence: ENSG00000298601 ENST00000756757.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.782
• Publications: 12 publications found

Genes affected

ENSG00000298601 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377171	XR_940977.4	n.215+27263C>T		intron_variant	Intron 2 of 6
LOC105377171	XR_940978.4	n.215+27263C>T		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298601	ENST00000756757.1	n.234+27263C>T		intron_variant	Intron 2 of 5
ENSG00000298601	ENST00000756759.1	n.189+27263C>T		intron_variant	Intron 2 of 5
ENSG00000298601	ENST00000756760.1	n.220+27263C>T		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51194 AN: 151406 Hom.: 8883 Cov.: 31

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.338 AC: 51244 AN: 151524 Hom.: 8900 Cov.: 31 AF XY: 0.334 AC XY: 24743 AN XY: 74034

African (AFR) AF: 0.353 AC: 14594 AN: 41322

American (AMR) AF: 0.243 AC: 3693 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1175 AN: 3460

East Asian (EAS) AF: 0.462 AC: 2363 AN: 5116

South Asian (SAS) AF: 0.231 AC: 1110 AN: 4808

European-Finnish (FIN) AF: 0.341 AC: 3581 AN: 10506

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23606 AN: 67808

Other (OTH) AF: 0.319 AC: 673 AN: 2108

Alfa AF: 0.347 Hom.: 32923

Bravo AF: 0.336

Asia WGS AF: 0.348 AC: 1209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.37
DANN	Benign	0.56
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs9836484; hg19: chr3-78044689;