ENST00000755297.1:n.32+12477C>T

Variant names:

• chr6-31283583-C-T
• rs3873375
• ENST00000755297.1:n.32+12477C>T

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.32+12477C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 152,108 control chromosomes in the GnomAD database, including 9,577 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 0.35 (9577 hom., cov: 33)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.252
• Publications: 20 publications found

Genes affected

ENSG00000298396 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.44 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
ENSG00000298396	ENST00000755297.1	n.32+12477C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.349 AC: 53100 AN: 151990 Hom.: 9565 Cov.: 33

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.349 AC: 53143 AN: 152108 Hom.: 9577 Cov.: 33 AF XY: 0.352 AC XY: 26183 AN XY: 74350

African (AFR) AF: 0.446 AC: 18488 AN: 41476

American (AMR) AF: 0.334 AC: 5102 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1032 AN: 3470

East Asian (EAS) AF: 0.306 AC: 1585 AN: 5176

South Asian (SAS) AF: 0.330 AC: 1592 AN: 4820

European-Finnish (FIN) AF: 0.392 AC: 4146 AN: 10570

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20105 AN: 67988

Other (OTH) AF: 0.346 AC: 729 AN: 2108

Alfa AF: 0.321 Hom.: 16060

Bravo AF: 0.348

Asia WGS AF: 0.311 AC: 1083 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.1
DANN	Benign	0.89
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs3873375; hg19: chr6-31251360;