18-79013973-C-T

Variant names:

• chr18-79013973-C-T
• rs7241993
• ENST00000836199.1:n.557+9915G>A

Variant summary

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

The ENST00000836199.1(ENSG00000308736):​n.557+9915G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 152,102 control chromosomes in the GnomAD database, including 11,421 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 0.37 (11421 hom., cov: 34)
• Consequence: ENSG00000308736 ENST00000836199.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710
• Publications: 50 publications found

Genes affected

ENSG00000308736 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000836199.1. 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
	ENSG00000308736	ENST00000836199.1		n.557+9915G>A		intron	N/A
	ENSG00000308736	ENST00000836200.1		n.450+9980G>A		intron	N/A
	ENSG00000308736	ENST00000836201.1		n.531+9915G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56744 AN: 151984 Hom.: 11402 Cov.: 34

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.373 AC: 56805 AN: 152102 Hom.: 11421 Cov.: 34 AF XY: 0.374 AC XY: 27796 AN XY: 74348

African (AFR) AF: 0.535 AC: 22190 AN: 41486

American (AMR) AF: 0.316 AC: 4829 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1132 AN: 3470

East Asian (EAS) AF: 0.401 AC: 2077 AN: 5176

South Asian (SAS) AF: 0.343 AC: 1654 AN: 4822

European-Finnish (FIN) AF: 0.299 AC: 3156 AN: 10552

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20583 AN: 67990

Other (OTH) AF: 0.359 AC: 758 AN: 2110

Alfa AF: 0.327 Hom.: 25835

Bravo AF: 0.382

Asia WGS AF: 0.370 AC: 1283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.73
DANN	Benign	0.46
PhyloP100		0.071

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: rs7241993;

hg19: chr18-76773973;