rs2523518

Variant names:

• chr6-31373351-T-G
• rs2523518
• ENST00000649421.2:n.275-1532T>G

Variant summary

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

The ENST00000649421.2(ENSG00000285647):​n.275-1532T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.848 in 151,054 control chromosomes in the GnomAD database, including 54,738 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 (54738 hom., cov: 30)
• Consequence: ENSG00000285647 ENST00000649421.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560
• Publications: 4 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=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.926 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.275-1532T>G		intron_variant	Intron 1 of 1
ENSG00000298426	ENST00000755446.1	n.327-8629T>G		intron_variant	Intron 1 of 1
ENSG00000285647	ENST00000755530.1	n.203-1532T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.848 AC: 128032 AN: 150938 Hom.: 54685 Cov.: 30

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.922

Gnomad AMR AF: 0.897

Gnomad ASJ AF: 0.931

Gnomad EAS AF: 0.949

Gnomad SAS AF: 0.933

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.923

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.879

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

GnomAD4 genome AF: 0.848 AC: 128141 AN: 151054 Hom.: 54738 Cov.: 30 AF XY: 0.852 AC XY: 62742 AN XY: 73664

African (AFR) AF: 0.837 AC: 34674 AN: 41444

American (AMR) AF: 0.897 AC: 13315 AN: 14844

Ashkenazi Jewish (ASJ) AF: 0.931 AC: 3229 AN: 3470

East Asian (EAS) AF: 0.949 AC: 4812 AN: 5072

South Asian (SAS) AF: 0.934 AC: 4273 AN: 4576

European-Finnish (FIN) AF: 0.836 AC: 8774 AN: 10494

Middle Eastern (MID) AF: 0.918 AC: 268 AN: 292

European-Non Finnish (NFE) AF: 0.827 AC: 56097 AN: 67842

Other (OTH) AF: 0.882 AC: 1862 AN: 2112

Alfa AF: 0.838 Hom.: 19848

Bravo AF: 0.851

Asia WGS AF: 0.924 AC: 3149 AN: 3406

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	14
DANN	Benign	0.89
PhyloP100		-0.056

Splicing

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

Other links and lift over

dbSNP: rs2523518; hg19: chr6-31341128;