ENST00000650971.1:n.569-1943T>C

Variant names:

• chr8-127632710-T-C
• rs4130120
• ENST00000650971.1:n.569-1943T>C

Variant summary

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

The ENST00000650971.1(ENSG00000286266):​n.569-1943T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,032 control chromosomes in the GnomAD database, including 2,842 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 (2842 hom., cov: 32)
• Consequence: ENSG00000286266 ENST00000650971.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 7 publications found

Genes affected

ENSG00000286266 (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 = 0.326 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
ENSG00000286266	ENST00000650971.1	n.569-1943T>C		intron_variant	Intron 3 of 4
ENSG00000286010	ENST00000754566.1	n.111-1233A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24030 AN: 151914 Hom.: 2828 Cov.: 32

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.0934

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.0612

Gnomad SAS AF: 0.0725

Gnomad FIN AF: 0.0553

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0946

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.158 AC: 24067 AN: 152032 Hom.: 2842 Cov.: 32 AF XY: 0.154 AC XY: 11420 AN XY: 74380

African (AFR) AF: 0.331 AC: 13693 AN: 41356

American (AMR) AF: 0.119 AC: 1826 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 354 AN: 3470

East Asian (EAS) AF: 0.0610 AC: 316 AN: 5180

South Asian (SAS) AF: 0.0730 AC: 352 AN: 4824

European-Finnish (FIN) AF: 0.0553 AC: 586 AN: 10596

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0945 AC: 6430 AN: 68008

Other (OTH) AF: 0.181 AC: 380 AN: 2104

Alfa AF: 0.110 Hom.: 2495

Bravo AF: 0.173

Asia WGS AF: 0.0900 AC: 314 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	1.5
DANN	Benign	0.44
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs4130120; hg19: chr8-128644955;