chr1-231465611-C-T

Variant names:

• chr1-231465611-C-T
• rs2790859
• ENST00000662216.1:c.-207-2937G>A

Variant summary

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

The ENST00000662216.1(ENSG00000287856):​c.-207-2937G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 151,998 control chromosomes in the GnomAD database, including 21,652 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 0.51 (21652 hom., cov: 32)
• Consequence: ENSG00000287856 ENST00000662216.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.57
• Publications: 9 publications found

Genes affected

ENSG00000287856 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662216.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287856	ENST00000662216.1		c.-207-2937G>A		intron	N/A	ENSP00000499467.1
	ENSG00000287856	ENST00000653908.1		c.-207-2937G>A		intron	N/A	ENSP00000499669.1
	ENSG00000287856	ENST00000653198.1		n.231-2937G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77962 AN: 151880 Hom.: 21595 Cov.: 32

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.514 AC: 78072 AN: 151998 Hom.: 21652 Cov.: 32 AF XY: 0.507 AC XY: 37646 AN XY: 74278

African (AFR) AF: 0.734 AC: 30456 AN: 41490

American (AMR) AF: 0.543 AC: 8296 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1321 AN: 3468

East Asian (EAS) AF: 0.526 AC: 2717 AN: 5168

South Asian (SAS) AF: 0.460 AC: 2214 AN: 4814

European-Finnish (FIN) AF: 0.309 AC: 3255 AN: 10530

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.416 AC: 28291 AN: 67948

Other (OTH) AF: 0.505 AC: 1064 AN: 2108

Alfa AF: 0.491 Hom.: 3065

Bravo AF: 0.543

Asia WGS AF: 0.507 AC: 1765 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.50
DANN	Benign	0.36
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs2790859; hg19: chr1-231601357;