ENST00000817320.1:n.284+18770C>T

Variant names:

• chr11-36729577-C-T
• rs1996537
• ENST00000817320.1:n.284+18770C>T

Variant summary

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

The ENST00000817320.1(ENSG00000306379):​n.284+18770C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 151,932 control chromosomes in the GnomAD database, including 2,442 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 0.17 (2442 hom., cov: 33)
• Consequence: ENSG00000306379 ENST00000817320.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170
• Publications: 2 publications found

Genes affected

ENSG00000306379 (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 (AFR) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000817320.1. 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
	ENSG00000306379	ENST00000817320.1		n.284+18770C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25890 AN: 151814 Hom.: 2442 Cov.: 33

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.170 AC: 25904 AN: 151932 Hom.: 2442 Cov.: 33 AF XY: 0.170 AC XY: 12610 AN XY: 74252

African (AFR) AF: 0.231 AC: 9587 AN: 41418

American (AMR) AF: 0.130 AC: 1983 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 428 AN: 3468

East Asian (EAS) AF: 0.162 AC: 839 AN: 5164

South Asian (SAS) AF: 0.111 AC: 532 AN: 4806

European-Finnish (FIN) AF: 0.163 AC: 1717 AN: 10536

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10330 AN: 67956

Other (OTH) AF: 0.157 AC: 332 AN: 2114

Alfa AF: 0.151 Hom.: 324

Bravo AF: 0.171

Asia WGS AF: 0.162 AC: 562 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.9
DANN	Benign	0.55
PhyloP100		0.017

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: rs1996537;

hg19: chr11-36751127;