6-31349570-C-T

Variant names:

• chr6-31349570-C-T
• rs2156875
• ENST00000755297.1:n.33-6631C>T

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.33-6631C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 151,972 control chromosomes in the GnomAD database, including 19,063 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 0.50 (19063 hom., cov: 32)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.625
• Publications: 37 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.508 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.33-6631C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.500 AC: 75883 AN: 151854 Hom.: 19055 Cov.: 32

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.500 AC: 75934 AN: 151972 Hom.: 19063 Cov.: 32 AF XY: 0.495 AC XY: 36784 AN XY: 74274

African (AFR) AF: 0.502 AC: 20802 AN: 41424

American (AMR) AF: 0.435 AC: 6646 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1524 AN: 3468

East Asian (EAS) AF: 0.502 AC: 2595 AN: 5172

South Asian (SAS) AF: 0.466 AC: 2244 AN: 4816

European-Finnish (FIN) AF: 0.539 AC: 5693 AN: 10556

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.513 AC: 34834 AN: 67940

Other (OTH) AF: 0.464 AC: 981 AN: 2112

Alfa AF: 0.510 Hom.: 76499

Bravo AF: 0.491

Asia WGS AF: 0.517 AC: 1798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	8.3
DANN	Benign	0.53
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs2156875; hg19: chr6-31317347;