22-36036289-A-T

Variant names:

• chr22-36036289-A-T
• rs739200
• ENST00000766372.1:n.174-1911A>T

Variant summary

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

The ENST00000766372.1(ENSG00000299784):​n.174-1911A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 152,108 control chromosomes in the GnomAD database, including 11,577 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 0.29 (11577 hom., cov: 31)
• Consequence: ENSG00000299784 ENST00000766372.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 3 publications found

Genes affected

ENSG00000299784 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299784	ENST00000766372.1	n.174-1911A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43551 AN: 151990 Hom.: 11531 Cov.: 31

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.0822

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0973

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.287 AC: 43652 AN: 152108 Hom.: 11577 Cov.: 31 AF XY: 0.277 AC XY: 20595 AN XY: 74354

African (AFR) AF: 0.712 AC: 29511 AN: 41460

American (AMR) AF: 0.145 AC: 2222 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 438 AN: 3472

East Asian (EAS) AF: 0.0824 AC: 427 AN: 5182

South Asian (SAS) AF: 0.119 AC: 574 AN: 4818

European-Finnish (FIN) AF: 0.0973 AC: 1031 AN: 10596

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8844 AN: 67978

Other (OTH) AF: 0.225 AC: 475 AN: 2108

Alfa AF: 0.0749 Hom.: 100

Bravo AF: 0.311

Asia WGS AF: 0.139 AC: 486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.63
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs739200; hg19: chr22-36432337;