ENST00000743650.1:n.372-120A>T

Variant names:

• chr6-156633907-T-A
• rs2817460
• ENST00000743650.1:n.372-120A>T

Variant summary

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

The ENST00000743650.1(ENSG00000296922):​n.372-120A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,178 control chromosomes in the GnomAD database, including 2,208 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 0.16 (2208 hom., cov: 33)
• Consequence: ENSG00000296922 ENST00000743650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289
• Publications: 2 publications found

Genes affected

ENSG00000296922 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.19 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
ENSG00000296922	ENST00000743650.1	n.372-120A>T		intron_variant	Intron 3 of 3
ENSG00000296922	ENST00000743651.1	n.369-120A>T		intron_variant	Intron 2 of 2
ENSG00000296922	ENST00000743652.1	n.282-120A>T		intron_variant	Intron 2 of 2
ENSG00000296922	ENST00000743653.1	n.150-120A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24481 AN: 152060 Hom.: 2209 Cov.: 33

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.161 AC: 24480 AN: 152178 Hom.: 2208 Cov.: 33 AF XY: 0.162 AC XY: 12017 AN XY: 74396

African (AFR) AF: 0.109 AC: 4542 AN: 41536

American (AMR) AF: 0.107 AC: 1636 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 532 AN: 3468

East Asian (EAS) AF: 0.143 AC: 738 AN: 5174

South Asian (SAS) AF: 0.113 AC: 543 AN: 4820

European-Finnish (FIN) AF: 0.268 AC: 2840 AN: 10580

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13106 AN: 67986

Other (OTH) AF: 0.143 AC: 302 AN: 2110

Alfa AF: 0.0948 Hom.: 181

Bravo AF: 0.146

Asia WGS AF: 0.178 AC: 621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.089
DANN	Benign	0.51
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs2817460; hg19: chr6-156955041; COSMIC: COSV60297138;