chr11-18793748-T-G

Variant names:

• chr11-18793748-T-G
• rs7932938
• ENST00000836338.1:n.162+2815T>G

Variant summary

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

The ENST00000836338.1(ENSG00000255244):​n.162+2815T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 152,028 control chromosomes in the GnomAD database, including 17,230 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 0.47 (17230 hom., cov: 32)
• Consequence: ENSG00000255244 ENST00000836338.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.745
• Publications: 4 publications found

Genes affected

ENSG00000255244 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000836338.1. 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
	ENSG00000255244	ENST00000836338.1		n.162+2815T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71253 AN: 151910 Hom.: 17235 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.469 AC: 71269 AN: 152028 Hom.: 17230 Cov.: 32 AF XY: 0.467 AC XY: 34679 AN XY: 74312

African (AFR) AF: 0.386 AC: 16023 AN: 41460

American (AMR) AF: 0.487 AC: 7435 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1317 AN: 3470

East Asian (EAS) AF: 0.270 AC: 1399 AN: 5176

South Asian (SAS) AF: 0.412 AC: 1987 AN: 4824

European-Finnish (FIN) AF: 0.549 AC: 5791 AN: 10556

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.526 AC: 35762 AN: 67960

Other (OTH) AF: 0.443 AC: 933 AN: 2104

Alfa AF: 0.501 Hom.: 80289

Bravo AF: 0.460

Asia WGS AF: 0.354 AC: 1233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	12
DANN	Benign	0.67
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs7932938; hg19: chr11-18815295;