1-231462872-A-G

Position:

• chr1-231462872-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000662216.1(ENSG00000287856):​c.-207-198T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 152,084 control chromosomes in the GnomAD database, including 8,816 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 0.32 (8816 hom., cov: 32)
• Consequence: ENSG00000287856 ENST00000662216.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

Genes affected

ENSG00000287856 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.231462872A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287856	ENST00000662216.1	c.-207-198T>C		intron_variant				ENSP00000499467.1
ENSG00000287856	ENST00000653908.1	c.-207-198T>C		intron_variant				ENSP00000499669.1
ENSG00000287856	ENST00000653198.1	n.231-198T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47935 AN: 151966 Hom.: 8785 Cov.: 32

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.0362

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.316 AC: 48011 AN: 152084 Hom.: 8816 Cov.: 32 AF XY: 0.305 AC XY: 22698 AN XY: 74368

Gnomad4 AFR AF: 0.493

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.0361

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.286

Alfa AF: 0.287 Hom.: 1684

Bravo AF: 0.341

Asia WGS AF: 0.113 AC: 397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1769792; hg19: chr1-231598618; COSMIC: COSV70605476;