18-62320408-T-C

Variant names:

• chr18-62320408-T-C
• rs6567263
• ENST00000756986.1:n.250+2960A>G

Variant summary

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

The ENST00000756986.1(ENSG00000267560):​n.250+2960A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 152,028 control chromosomes in the GnomAD database, including 5,915 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 0.27 (5915 hom., cov: 32)
• Consequence: ENSG00000267560 ENST00000756986.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.562
• Publications: 8 publications found

Genes affected

ENSG00000267560 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.331 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
ENSG00000267560	ENST00000756986.1	n.250+2960A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41377 AN: 151910 Hom.: 5914 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.272 AC: 41393 AN: 152028 Hom.: 5915 Cov.: 32 AF XY: 0.268 AC XY: 19915 AN XY: 74302

African (AFR) AF: 0.336 AC: 13921 AN: 41452

American (AMR) AF: 0.226 AC: 3455 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 805 AN: 3470

East Asian (EAS) AF: 0.103 AC: 533 AN: 5178

South Asian (SAS) AF: 0.165 AC: 792 AN: 4810

European-Finnish (FIN) AF: 0.252 AC: 2668 AN: 10580

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.269 AC: 18296 AN: 67940

Other (OTH) AF: 0.273 AC: 576 AN: 2110

Alfa AF: 0.204 Hom.: 633

Bravo AF: 0.273

Asia WGS AF: 0.165 AC: 574 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.3
DANN	Benign	0.66
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs6567263; hg19: chr18-59987641;