chr1-22641003-G-A

Variant names:

• chr1-22641003-G-A
• rs6690827
• ENST00000695747.1:c.492+1842G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

Genes affected

ENSG00000289692 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289692	ENST00000695747.1	c.492+1842G>A		intron_variant	Intron 3 of 4			ENSP00000512140.1
ENSG00000289692	ENST00000695748.1	c.492+1842G>A		intron_variant	Intron 3 of 3			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

African (AFR) AF: 0.427 AC: 17659 AN: 41396

American (AMR) AF: 0.438 AC: 6696 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1046 AN: 3468

East Asian (EAS) AF: 0.449 AC: 2305 AN: 5132

South Asian (SAS) AF: 0.451 AC: 2163 AN: 4800

European-Finnish (FIN) AF: 0.304 AC: 3217 AN: 10582

Middle Eastern (MID) AF: 0.269 AC: 78 AN: 290

European-Non Finnish (NFE) AF: 0.304 AC: 20683 AN: 67938

Other (OTH) AF: 0.360 AC: 759 AN: 2108

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
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs6690827; hg19: chr1-22967496;