chr6-31286311-T-C

Variant names:

• chr6-31286311-T-C
• rs2853933
• ENST00000755297.1:n.32+15205T>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+15205T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.658 in 152,094 control chromosomes in the GnomAD database, including 33,225 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 0.66 (33225 hom., cov: 32)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01
• Publications: 29 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.728 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+15205T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.658 AC: 99931 AN: 151976 Hom.: 33184 Cov.: 32

Gnomad AFR AF: 0.735

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.658 AC: 100025 AN: 152094 Hom.: 33225 Cov.: 32 AF XY: 0.663 AC XY: 49243 AN XY: 74328

African (AFR) AF: 0.735 AC: 30490 AN: 41510

American (AMR) AF: 0.718 AC: 10968 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.581 AC: 2017 AN: 3472

East Asian (EAS) AF: 0.722 AC: 3734 AN: 5170

South Asian (SAS) AF: 0.688 AC: 3317 AN: 4820

European-Finnish (FIN) AF: 0.669 AC: 7068 AN: 10560

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40363 AN: 67966

Other (OTH) AF: 0.681 AC: 1437 AN: 2110

Alfa AF: 0.616 Hom.: 113081

Bravo AF: 0.666

Asia WGS AF: 0.713 AC: 2481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.2
DANN	Benign	0.37
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs2853933; hg19: chr6-31254088;