6-31374854-T-C

Variant names:

• chr6-31374854-T-C
• rs2254556
• ENST00000649421.2:n.275-29T>C

Variant summary

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

The ENST00000649421.2(ENSG00000285647):​n.275-29T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.851 in 152,240 control chromosomes in the GnomAD database, including 55,273 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 0.85 (55273 hom., cov: 32)
• Consequence: ENSG00000285647 ENST00000649421.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 23 publications found

Genes affected

ENSG00000285647 (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 (EAS) allele frequency at 95% confidence interval = 0.929 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
ENSG00000285647	ENST00000649421.2	n.275-29T>C		intron_variant	Intron 1 of 1
ENSG00000298426	ENST00000755446.1	n.327-7126T>C		intron_variant	Intron 1 of 1
ENSG00000285647	ENST00000755530.1	n.203-29T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.851 AC: 129478 AN: 152122 Hom.: 55219 Cov.: 32

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.922

Gnomad AMR AF: 0.904

Gnomad ASJ AF: 0.931

Gnomad EAS AF: 0.951

Gnomad SAS AF: 0.940

Gnomad FIN AF: 0.840

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.882

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

GnomAD4 genome AF: 0.851 AC: 129588 AN: 152240 Hom.: 55273 Cov.: 32 AF XY: 0.855 AC XY: 63638 AN XY: 74426

African (AFR) AF: 0.837 AC: 34781 AN: 41536

American (AMR) AF: 0.905 AC: 13835 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.931 AC: 3233 AN: 3472

East Asian (EAS) AF: 0.951 AC: 4942 AN: 5194

South Asian (SAS) AF: 0.940 AC: 4539 AN: 4828

European-Finnish (FIN) AF: 0.840 AC: 8884 AN: 10582

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.829 AC: 56394 AN: 68016

Other (OTH) AF: 0.884 AC: 1867 AN: 2112

Alfa AF: 0.843 Hom.: 62374

Bravo AF: 0.853

Asia WGS AF: 0.936 AC: 3257 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	1.6
DANN	Benign	0.63
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs2254556; hg19: chr6-31342631;