chr18-29884999-C-T

Variant names:

• chr18-29884999-C-T
• rs958727
• ENST00000803180.1:n.164+36665G>A

Variant summary

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

The ENST00000803180.1(ENSG00000304402):​n.164+36665G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.022 in 152,042 control chromosomes in the GnomAD database, including 90 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 0.022 (90 hom., cov: 32)
• Consequence: ENSG00000304402 ENST00000803180.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.462
• Publications: 0 publications found

Genes affected

ENSG00000304402 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0898 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000803180.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304402	ENST00000803180.1		n.164+36665G>A		intron	N/A
	ENSG00000304402	ENST00000803181.1		n.164+36665G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0220 AC: 3339 AN: 151924 Hom.: 90 Cov.: 32

Gnomad AFR AF: 0.0337

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0429

Gnomad ASJ AF: 0.00836

Gnomad EAS AF: 0.00406

Gnomad SAS AF: 0.0968

Gnomad FIN AF: 0.00817

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00933

Gnomad OTH AF: 0.0215

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

GnomAD4 genome AF: 0.0220 AC: 3344 AN: 152042 Hom.: 90 Cov.: 32 AF XY: 0.0235 AC XY: 1744 AN XY: 74330

African (AFR) AF: 0.0336 AC: 1396 AN: 41492

American (AMR) AF: 0.0431 AC: 659 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.00836 AC: 29 AN: 3470

East Asian (EAS) AF: 0.00407 AC: 21 AN: 5162

South Asian (SAS) AF: 0.0971 AC: 468 AN: 4820

European-Finnish (FIN) AF: 0.00817 AC: 86 AN: 10528

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00933 AC: 634 AN: 67976

Other (OTH) AF: 0.0208 AC: 44 AN: 2112

Alfa AF: 0.00842 Hom.: 2

Bravo AF: 0.0240

Asia WGS AF: 0.0640 AC: 219 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.40
DANN	Benign	0.24
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs958727; hg19: chr18-27464964;