6-31353434-C-T

Variant names:

• chr6-31353434-C-T
• rs2596501
• ENST00000755297.1:n.33-2767C>T

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.33-2767C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.567 in 151,816 control chromosomes in the GnomAD database, including 25,001 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 0.57 (25001 hom., cov: 30)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355
• Publications: 55 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.669 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.33-2767C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.567 AC: 85964 AN: 151698 Hom.: 24971 Cov.: 30

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.732

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.567 AC: 86051 AN: 151816 Hom.: 25001 Cov.: 30 AF XY: 0.570 AC XY: 42315 AN XY: 74200

African (AFR) AF: 0.633 AC: 26173 AN: 41326

American (AMR) AF: 0.680 AC: 10381 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 2649 AN: 3470

East Asian (EAS) AF: 0.495 AC: 2562 AN: 5176

South Asian (SAS) AF: 0.674 AC: 3240 AN: 4810

European-Finnish (FIN) AF: 0.494 AC: 5202 AN: 10538

Middle Eastern (MID) AF: 0.736 AC: 212 AN: 288

European-Non Finnish (NFE) AF: 0.498 AC: 33820 AN: 67930

Other (OTH) AF: 0.620 AC: 1303 AN: 2100

Alfa AF: 0.536 Hom.: 63969

Bravo AF: 0.585

Asia WGS AF: 0.653 AC: 2269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	11
DANN	Benign	0.30
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs2596501; hg19: chr6-31321211;