ENST00000755297.1:n.32+2244T>C

Variant names:

• chr6-31273350-T-C
• rs13207315
• ENST00000755297.1:n.32+2244T>C

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.32+2244T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 151,860 control chromosomes in the GnomAD database, including 1,491 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 0.13 (1491 hom., cov: 31)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.799
• Publications: 12 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=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.231 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+2244T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20045 AN: 151742 Hom.: 1489 Cov.: 31

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.132 AC: 20054 AN: 151860 Hom.: 1491 Cov.: 31 AF XY: 0.134 AC XY: 9946 AN XY: 74232

African (AFR) AF: 0.107 AC: 4413 AN: 41396

American (AMR) AF: 0.117 AC: 1785 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1205 AN: 3468

East Asian (EAS) AF: 0.107 AC: 550 AN: 5148

South Asian (SAS) AF: 0.242 AC: 1162 AN: 4800

European-Finnish (FIN) AF: 0.101 AC: 1071 AN: 10556

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9315 AN: 67924

Other (OTH) AF: 0.137 AC: 289 AN: 2104

Alfa AF: 0.128 Hom.: 352

Bravo AF: 0.129

Asia WGS AF: 0.141 AC: 491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.4
DANN	Benign	0.26
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs13207315; hg19: chr6-31241127;