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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372225	XR_001753513.2	n.338+9915G>A		intron_variant	Intron 2 of 2
LOC105372225	XR_001753514.2	n.226+9915G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308736	ENST00000836199.1	n.557+9915G>A		intron_variant	Intron 2 of 2
ENSG00000308736	ENST00000836200.1	n.450+9980G>A		intron_variant	Intron 2 of 2
ENSG00000308736	ENST00000836201.1	n.531+9915G>A		intron_variant	Intron 2 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs7241993; hg19: chr18-76773973;