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. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650684.1(ENSG00000293110):​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: ENSG00000293110 ENST00000650684.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 40 publications found

Genes affected

ENSG00000293110 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000293110	ENST00000650684.1	n.1074-26413T>G		intron_variant	Intron 8 of 8
ENSG00000293110	ENST00000650727.1	n.1044-26413T>G		intron_variant	Intron 8 of 14
ENSG00000293110	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

African (AFR) AF: 0.0564 AC: 2342 AN: 41518

American (AMR) AF: 0.138 AC: 2110 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 574 AN: 3470

East Asian (EAS) AF: 0.0203 AC: 105 AN: 5170

South Asian (SAS) AF: 0.192 AC: 926 AN: 4816

European-Finnish (FIN) AF: 0.175 AC: 1848 AN: 10570

Middle Eastern (MID) AF: 0.110 AC: 32 AN: 292

European-Non Finnish (NFE) AF: 0.246 AC: 16709 AN: 67974

Other (OTH) AF: 0.166 AC: 350 AN: 2114

Alfa AF: 0.212 Hom.: 9365

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
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs13204965; hg19: chr6-127167072;