1-82731525-C-T

Variant names:

• chr1-82731525-C-T
• rs919876
• ENST00000650063.1:n.266-46952G>A

Variant summary

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

The ENST00000650063.1(ENSG00000233290):​n.266-46952G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.947 in 151,868 control chromosomes in the GnomAD database, including 68,277 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 0.95 (68277 hom., cov: 31)
• Consequence: ENSG00000233290 ENST00000650063.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335
• Publications: 0 publications found

Genes affected

ENSG00000233290 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650063.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000233290	ENST00000650063.1		n.266-46952G>A		intron	N/A
	ENSG00000233290	ENST00000653483.1		n.98-46952G>A		intron	N/A
	ENSG00000233290	ENST00000663002.2		n.94-75437G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.947 AC: 143726 AN: 151750 Hom.: 68238 Cov.: 31

Gnomad AFR AF: 0.879

Gnomad AMI AF: 0.982

Gnomad AMR AF: 0.971

Gnomad ASJ AF: 0.911

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.941

Gnomad FIN AF: 0.990

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.975

Gnomad OTH AF: 0.951

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

GnomAD4 genome AF: 0.947 AC: 143817 AN: 151868 Hom.: 68277 Cov.: 31 AF XY: 0.949 AC XY: 70433 AN XY: 74222

African (AFR) AF: 0.879 AC: 36448 AN: 41472

American (AMR) AF: 0.971 AC: 14787 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.911 AC: 3158 AN: 3466

East Asian (EAS) AF: 0.997 AC: 5107 AN: 5120

South Asian (SAS) AF: 0.940 AC: 4532 AN: 4822

European-Finnish (FIN) AF: 0.990 AC: 10402 AN: 10512

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.975 AC: 66194 AN: 67926

Other (OTH) AF: 0.952 AC: 2008 AN: 2110

Alfa AF: 0.955 Hom.: 8444

Bravo AF: 0.944

Asia WGS AF: 0.961 AC: 3324 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.89
DANN	Benign	0.22
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs919876; hg19: chr1-83197208;