18-62321458-G-A

Variant names:

• chr18-62321458-G-A
• rs7226991
• ENST00000756986.1:n.250+1910C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000756986.1(ENSG00000267560):​n.250+1910C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 151,118 control chromosomes in the GnomAD database, including 7,058 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 0.30 (7058 hom., cov: 30)
• Consequence: ENSG00000267560 ENST00000756986.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238
• Publications: 11 publications found

Genes affected

ENSG00000267560 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000756986.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000267560	ENST00000756986.1		n.250+1910C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45049 AN: 151000 Hom.: 7056 Cov.: 30

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.298 AC: 45066 AN: 151118 Hom.: 7058 Cov.: 30 AF XY: 0.294 AC XY: 21646 AN XY: 73690

African (AFR) AF: 0.372 AC: 15275 AN: 41092

American (AMR) AF: 0.248 AC: 3754 AN: 15150

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 874 AN: 3466

East Asian (EAS) AF: 0.107 AC: 548 AN: 5140

South Asian (SAS) AF: 0.195 AC: 932 AN: 4770

European-Finnish (FIN) AF: 0.268 AC: 2782 AN: 10370

Middle Eastern (MID) AF: 0.312 AC: 91 AN: 292

European-Non Finnish (NFE) AF: 0.293 AC: 19909 AN: 67836

Other (OTH) AF: 0.300 AC: 629 AN: 2094

Alfa AF: 0.268 Hom.: 3024

Bravo AF: 0.299

Asia WGS AF: 0.183 AC: 635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	7.5
DANN	Benign	0.75
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs7226991; hg19: chr18-59988691;