chr1-231462787-C-T

Variant names:

• chr1-231462787-C-T
• rs961154
• ENST00000662216.1:c.-207-113G>A

Variant summary

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

The ENST00000662216.1(ENSG00000287856):​c.-207-113G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 151,962 control chromosomes in the GnomAD database, including 24,007 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 0.55 (24007 hom., cov: 32)
• Consequence: ENSG00000287856 ENST00000662216.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500
• Publications: 8 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.734 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

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
	ENSG00000287856	ENST00000662216.1		c.-207-113G>A		intron	N/A	ENSP00000499467.1	A0A590UJK7
	ENSG00000287856	ENST00000653908.1		c.-207-113G>A		intron	N/A	ENSP00000499669.1	A0A590UK27
	ENSG00000287856	ENST00000653198.1		n.231-113G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83282 AN: 151844 Hom.: 23954 Cov.: 32

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.549 AC: 83388 AN: 151962 Hom.: 24007 Cov.: 32 AF XY: 0.543 AC XY: 40329 AN XY: 74260

African (AFR) AF: 0.741 AC: 30757 AN: 41510

American (AMR) AF: 0.571 AC: 8722 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1387 AN: 3470

East Asian (EAS) AF: 0.527 AC: 2721 AN: 5162

South Asian (SAS) AF: 0.466 AC: 2229 AN: 4780

European-Finnish (FIN) AF: 0.410 AC: 4313 AN: 10514

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31591 AN: 67934

Other (OTH) AF: 0.529 AC: 1118 AN: 2112

Alfa AF: 0.496 Hom.: 28544

Bravo AF: 0.572

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.46
PhyloP100		0.0050

Splicing

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

Other links and lift over

dbSNP: rs961154; hg19: chr1-231598533;