ENST00000733295.1:n.261+1028T>G

Variant names:

• chr10-124384503-A-C
• rs2807064
• ENST00000733295.1:n.261+1028T>G

Variant summary

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

The ENST00000733295.1(ENSG00000295867):​n.261+1028T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0925 in 152,132 control chromosomes in the GnomAD database, including 1,031 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 0.093 (1031 hom., cov: 33)
• Consequence: ENSG00000295867 ENST00000733295.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 1 publications found

Genes affected

ENSG00000295867 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000733295.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295867	ENST00000733295.1		n.261+1028T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0925 AC: 14067 AN: 152014 Hom.: 1029 Cov.: 33

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0608

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.0774

Gnomad SAS AF: 0.0788

Gnomad FIN AF: 0.0942

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0460

Gnomad OTH AF: 0.0708

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

GnomAD4 genome AF: 0.0925 AC: 14079 AN: 152132 Hom.: 1031 Cov.: 33 AF XY: 0.0932 AC XY: 6935 AN XY: 74400

African (AFR) AF: 0.186 AC: 7702 AN: 41426

American (AMR) AF: 0.0606 AC: 927 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 353 AN: 3472

East Asian (EAS) AF: 0.0774 AC: 400 AN: 5170

South Asian (SAS) AF: 0.0793 AC: 383 AN: 4830

European-Finnish (FIN) AF: 0.0942 AC: 999 AN: 10610

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0460 AC: 3131 AN: 68014

Other (OTH) AF: 0.0701 AC: 148 AN: 2112

Alfa AF: 0.0514 Hom.: 168

Bravo AF: 0.0951

Asia WGS AF: 0.0770 AC: 266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.79
DANN	Benign	0.34
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2807064; hg19: chr10-126073072;