18-28479148-T-C

Variant names:

• chr18-28479148-T-C
• rs4131805
• ENST00000767551.1:n.396-18139T>C

Variant summary

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

The ENST00000767551.1(ENSG00000299932):​n.396-18139T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 151,782 control chromosomes in the GnomAD database, including 9,979 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 0.32 (9979 hom., cov: 31)
• Consequence: ENSG00000299932 ENST00000767551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 5 publications found

Genes affected

ENSG00000299932 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000767551.1. 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
	ENSG00000299932	ENST00000767551.1		n.396-18139T>C		intron	N/A
	ENSG00000299932	ENST00000767552.1		n.735-18139T>C		intron	N/A
	ENSG00000299932	ENST00000767553.1		n.279-18139T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49259 AN: 151664 Hom.: 9959 Cov.: 31

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.0659

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.325 AC: 49324 AN: 151782 Hom.: 9979 Cov.: 31 AF XY: 0.319 AC XY: 23688 AN XY: 74166

African (AFR) AF: 0.575 AC: 23778 AN: 41326

American (AMR) AF: 0.269 AC: 4104 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 554 AN: 3470

East Asian (EAS) AF: 0.164 AC: 843 AN: 5138

South Asian (SAS) AF: 0.198 AC: 950 AN: 4808

European-Finnish (FIN) AF: 0.184 AC: 1939 AN: 10558

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16406 AN: 67902

Other (OTH) AF: 0.298 AC: 629 AN: 2114

Alfa AF: 0.269 Hom.: 15788

Bravo AF: 0.343

Asia WGS AF: 0.210 AC: 732 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.0
DANN	Benign	0.53
PhyloP100		0.31

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4131805;

hg19: chr18-26059112;