rs961154

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000287856 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000287856	ENST00000662216.1	c.-207-113G>A		intron_variant	Intron 2 of 6			ENSP00000499467.1
ENSG00000287856	ENST00000653908.1	c.-207-113G>A		intron_variant	Intron 1 of 4			ENSP00000499669.1
ENSG00000287856	ENST00000653198.1	n.231-113G>A		intron_variant	Intron 3 of 7

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

Gnomad4 AFR AF: 0.741

Gnomad4 AMR AF: 0.571

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.527

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.529

Alfa AF: 0.485 Hom.: 16658

Bravo AF: 0.572

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs961154; hg19: chr1-231598533;