1-22640116-C-G

Variant names:

• chr1-22640116-C-G
• rs12033074
• ENST00000695747.1:c.492+955C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000695747.1(ENSG00000289692):​c.492+955C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 152,096 control chromosomes in the GnomAD database, including 10,307 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 (10307 hom., cov: 32)
• Consequence: ENSG00000289692 ENST00000695747.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.770
• Publications: 8 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=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.436 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+955C>G		intron_variant	Intron 3 of 4			ENSP00000512140.1
ENSG00000289692	ENST00000695748.1	c.492+955C>G		intron_variant	Intron 3 of 3			ENSP00000512141.1

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54789 AN: 151978 Hom.: 10282 Cov.: 32

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.361 AC: 54863 AN: 152096 Hom.: 10307 Cov.: 32 AF XY: 0.366 AC XY: 27202 AN XY: 74344

African (AFR) AF: 0.427 AC: 17711 AN: 41472

American (AMR) AF: 0.438 AC: 6702 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1046 AN: 3470

East Asian (EAS) AF: 0.449 AC: 2327 AN: 5182

South Asian (SAS) AF: 0.452 AC: 2177 AN: 4816

European-Finnish (FIN) AF: 0.303 AC: 3204 AN: 10562

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20702 AN: 67982

Other (OTH) AF: 0.361 AC: 764 AN: 2114

Alfa AF: 0.200 Hom.: 440

Bravo AF: 0.373

Asia WGS AF: 0.485 AC: 1686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.028
DANN	Benign	0.43
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs12033074; hg19: chr1-22966609;