ENST00000650684.1:n.1074-26413T>G

Variant names:

• chr6-126845927-A-C
• rs13204965
• ENST00000650684.1:n.1074-26413T>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650684.1(ENSG00000286215):​n.1074-26413T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,114 control chromosomes in the GnomAD database, including 2,736 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 (2736 hom., cov: 32)
• Consequence: ENSG00000286215 ENST00000650684.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89

Genes affected

ENSG00000286215 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.243 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
ENSG00000286215	ENST00000650684.1	n.1074-26413T>G		intron_variant	Intron 8 of 8
ENSG00000286215	ENST00000650727.1	n.1044-26413T>G		intron_variant	Intron 8 of 14
ENSG00000286215	ENST00000650823.1	n.1129-26413T>G		intron_variant	Intron 9 of 11

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25226 AN: 151996 Hom.: 2734 Cov.: 32

Gnomad AFR AF: 0.0566

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.0205

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.166 AC: 25230 AN: 152114 Hom.: 2736 Cov.: 32 AF XY: 0.160 AC XY: 11920 AN XY: 74346

Gnomad4 AFR AF: 0.0564

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.0203

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.166

Alfa AF: 0.208 Hom.: 2841

Bravo AF: 0.154

Asia WGS AF: 0.141 AC: 490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.81
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13204965; hg19: chr6-127167072;