rs1769792

Variant names:

• chr1-231462872-A-G
• rs1769792
• ENST00000662216.1:c.-207-198T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-231462872-A-G
• chr1-231462872-A-T

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.487 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287856	ENST00000662216.1		c.-207-198T>C		intron	N/A	ENSP00000499467.1
	ENSG00000287856	ENST00000653908.1		c.-207-198T>C		intron	N/A	ENSP00000499669.1
	ENSG00000287856	ENST00000653198.1		n.231-198T>C		intron	N/A

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

African (AFR) AF: 0.493 AC: 20432 AN: 41444

American (AMR) AF: 0.334 AC: 5110 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 799 AN: 3472

East Asian (EAS) AF: 0.0361 AC: 187 AN: 5184

South Asian (SAS) AF: 0.120 AC: 578 AN: 4826

European-Finnish (FIN) AF: 0.183 AC: 1939 AN: 10586

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 18033 AN: 67978

Other (OTH) AF: 0.286 AC: 603 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.76
PhyloP100		-1.1

Splicing

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

Other links and lift over

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