chr18-59420051-T-A

Variant names:

• chr18-59420051-T-A
• rs9319950
• ENST00000767781.1:n.215-3621T>A

Variant summary

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

The ENST00000767781.1(ENSG00000299980):​n.215-3621T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 152,052 control chromosomes in the GnomAD database, including 12,367 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 0.38 (12367 hom., cov: 32)
• Consequence: ENSG00000299980 ENST00000767781.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130
• Publications: 1 publications found

Genes affected

ENSG00000299980 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000767781.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299980	ENST00000767781.1		n.215-3621T>A		intron	N/A
	ENSG00000299980	ENST00000767782.1		n.118-3621T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.382 AC: 58005 AN: 151934 Hom.: 12362 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.382 AC: 58024 AN: 152052 Hom.: 12367 Cov.: 32 AF XY: 0.391 AC XY: 29035 AN XY: 74314

African (AFR) AF: 0.191 AC: 7932 AN: 41502

American (AMR) AF: 0.435 AC: 6640 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1339 AN: 3468

East Asian (EAS) AF: 0.715 AC: 3691 AN: 5162

South Asian (SAS) AF: 0.529 AC: 2547 AN: 4816

European-Finnish (FIN) AF: 0.506 AC: 5349 AN: 10562

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.427 AC: 29049 AN: 67954

Other (OTH) AF: 0.393 AC: 827 AN: 2106

Alfa AF: 0.407 Hom.: 1763

Bravo AF: 0.368

Asia WGS AF: 0.571 AC: 1985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	9.6
DANN	Benign	0.87
PhyloP100		-0.013

Splicing

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

Other links and lift over

dbSNP: rs9319950; hg19: chr18-57087283;