chr6-31273760-C-T

Variant names:

• chr6-31273760-C-T
• rs2844621
• ENST00000755297.1:n.32+2654C>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+2654C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.742 in 152,084 control chromosomes in the GnomAD database, including 41,974 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 0.74 (41974 hom., cov: 32)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.653
• Publications: 21 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=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.78 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+2654C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.742 AC: 112716 AN: 151968 Hom.: 41924 Cov.: 32

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.801

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.752

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

GnomAD4 genome AF: 0.742 AC: 112824 AN: 152084 Hom.: 41974 Cov.: 32 AF XY: 0.748 AC XY: 55614 AN XY: 74356

African (AFR) AF: 0.751 AC: 31151 AN: 41454

American (AMR) AF: 0.745 AC: 11387 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.791 AC: 2745 AN: 3470

East Asian (EAS) AF: 0.727 AC: 3764 AN: 5178

South Asian (SAS) AF: 0.801 AC: 3866 AN: 4828

European-Finnish (FIN) AF: 0.795 AC: 8402 AN: 10572

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.721 AC: 49014 AN: 67986

Other (OTH) AF: 0.752 AC: 1580 AN: 2102

Alfa AF: 0.737 Hom.: 111709

Bravo AF: 0.738

Asia WGS AF: 0.782 AC: 2717 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.6
DANN	Benign	0.25
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs2844621; hg19: chr6-31241537;