6-31372551-T-C

Variant names:

• chr6-31372551-T-C
• rs2523522
• ENST00000649421.2:n.275-2332T>C

Variant summary

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

The ENST00000649421.2(ENSG00000285647):​n.275-2332T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 150,948 control chromosomes in the GnomAD database, including 25,450 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 (25450 hom., cov: 31)
• Consequence: ENSG00000285647 ENST00000649421.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.71
• Publications: 14 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=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.697 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.275-2332T>C		intron_variant	Intron 1 of 1
ENSG00000298426	ENST00000755446.1	n.327-9429T>C		intron_variant	Intron 1 of 1
ENSG00000285647	ENST00000755530.1	n.203-2332T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.568 AC: 85744 AN: 150836 Hom.: 25432 Cov.: 31

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.603

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.568 AC: 85798 AN: 150948 Hom.: 25450 Cov.: 31 AF XY: 0.566 AC XY: 41659 AN XY: 73626

African (AFR) AF: 0.501 AC: 20704 AN: 41364

American (AMR) AF: 0.515 AC: 7670 AN: 14906

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1432 AN: 3470

East Asian (EAS) AF: 0.716 AC: 3636 AN: 5078

South Asian (SAS) AF: 0.656 AC: 3037 AN: 4630

European-Finnish (FIN) AF: 0.512 AC: 5350 AN: 10440

Middle Eastern (MID) AF: 0.601 AC: 173 AN: 288

European-Non Finnish (NFE) AF: 0.620 AC: 42023 AN: 67762

Other (OTH) AF: 0.590 AC: 1240 AN: 2100

Alfa AF: 0.606 Hom.: 55093

Bravo AF: 0.564

Asia WGS AF: 0.640 AC: 2180 AN: 3404

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.23
DANN	Benign	0.28
PhyloP100		-5.7

Splicing

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

Other links and lift over

dbSNP: rs2523522; hg19: chr6-31340328;