rs6690827

Positions:

• chr1-22641003-G-A

Variant summary

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

The ENST00000695747.1(ENSG00000289692):​c.492+1842G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 151,904 control chromosomes in the GnomAD database, including 10,274 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 0.36 (10274 hom., cov: 31)
• Consequence: ENSG00000289692 ENST00000695747.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.839

Genes affected

ENSG00000289692 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.22641003G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000289692	ENST00000695747.1	c.492+1842G>A		intron_variant				ENSP00000512140.1
ENSG00000289692	ENST00000695748.1	c.492+1842G>A		intron_variant				ENSP00000512141.1

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54682 AN: 151786 Hom.: 10249 Cov.: 31

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.360 AC: 54756 AN: 151904 Hom.: 10274 Cov.: 31 AF XY: 0.366 AC XY: 27152 AN XY: 74248

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.304

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.360

Alfa AF: 0.334 Hom.: 1369

Bravo AF: 0.373

Asia WGS AF: 0.485 AC: 1684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.10
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6690827; hg19: chr1-22967496;