6-50853227-T-C

Variant names:

• chr6-50853227-T-C
• rs2635727
• ENST00000791176.1:n.275+442T>C

Variant summary

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

The ENST00000791176.1(ENSG00000303025):​n.275+442T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.743 in 152,076 control chromosomes in the GnomAD database, including 41,952 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 (41952 hom., cov: 32)
• Consequence: ENSG00000303025 ENST00000791176.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 20 publications found

Genes affected

ENSG00000303025 (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 (EAS) allele frequency at 95% confidence interval = 0.778 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
ENSG00000303025	ENST00000791176.1	n.275+442T>C		intron_variant	Intron 2 of 3
ENSG00000303025	ENST00000791177.1	n.324+442T>C		intron_variant	Intron 2 of 3
ENSG00000303025	ENST00000791178.1	n.289+442T>C		intron_variant	Intron 2 of 3
ENSG00000303025	ENST00000791179.1	n.201+2367T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.743 AC: 112863 AN: 151956 Hom.: 41915 Cov.: 32

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.798

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.720

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

GnomAD4 genome AF: 0.743 AC: 112955 AN: 152076 Hom.: 41952 Cov.: 32 AF XY: 0.740 AC XY: 55051 AN XY: 74348

African (AFR) AF: 0.729 AC: 30246 AN: 41470

American (AMR) AF: 0.765 AC: 11694 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.657 AC: 2280 AN: 3470

East Asian (EAS) AF: 0.798 AC: 4129 AN: 5172

South Asian (SAS) AF: 0.707 AC: 3414 AN: 4826

European-Finnish (FIN) AF: 0.728 AC: 7690 AN: 10568

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.752 AC: 51089 AN: 67970

Other (OTH) AF: 0.723 AC: 1529 AN: 2114

Alfa AF: 0.745 Hom.: 174791

Bravo AF: 0.745

Asia WGS AF: 0.775 AC: 2693 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	0.48
DANN	Benign	0.60
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2635727; hg19: chr6-50820940;