chr1-22298753-A-C

Variant names:

• chr1-22298753-A-C
• rs10799746
• ENST00000788801.1:n.452+10226A>C

Variant summary

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

The ENST00000788801.1(ENSG00000302675):​n.452+10226A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 151,916 control chromosomes in the GnomAD database, including 5,137 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 0.24 (5137 hom., cov: 32)
• Consequence: ENSG00000302675 ENST00000788801.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.128
• Publications: 6 publications found

Genes affected

ENSG00000302675 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000788801.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302675	ENST00000788801.1		n.452+10226A>C		intron	N/A
	ENSG00000302675	ENST00000788802.1		n.341+10226A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36318 AN: 151798 Hom.: 5120 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.0927

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.240 AC: 36387 AN: 151916 Hom.: 5137 Cov.: 32 AF XY: 0.242 AC XY: 17931 AN XY: 74240

African (AFR) AF: 0.387 AC: 16039 AN: 41420

American (AMR) AF: 0.236 AC: 3592 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 358 AN: 3462

East Asian (EAS) AF: 0.335 AC: 1725 AN: 5152

South Asian (SAS) AF: 0.0926 AC: 445 AN: 4806

European-Finnish (FIN) AF: 0.234 AC: 2468 AN: 10556

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11101 AN: 67958

Other (OTH) AF: 0.220 AC: 464 AN: 2110

Alfa AF: 0.183 Hom.: 12518

Bravo AF: 0.251

Asia WGS AF: 0.220 AC: 763 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.7
DANN	Benign	0.42
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs10799746; hg19: chr1-22625246; COSMIC: COSV59931054;