1-119526309-C-A

Variant names:

• chr1-119526309-C-A
• rs10802107
• ENST00000632456.2:n.242+28991G>T

Variant summary

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

The ENST00000756941.1(ENSG00000293080):​n.218+28991G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,152 control chromosomes in the GnomAD database, including 2,720 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 0.18 (2720 hom., cov: 32)
• Consequence: ENSG00000293080 ENST00000756941.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303
• Publications: 3 publications found

Genes affected

ENSG00000293080 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000756941.1. 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
	ENSG00000293080	ENST00000632456.2	TSL:6	n.242+28991G>T		intron	N/A
	ENSG00000293080	ENST00000756941.1		n.218+28991G>T		intron	N/A
	ENSG00000293080	ENST00000756942.1		n.258+28991G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27041 AN: 152034 Hom.: 2723 Cov.: 32

Gnomad AFR AF: 0.0809

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.0841

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.178 AC: 27039 AN: 152152 Hom.: 2720 Cov.: 32 AF XY: 0.176 AC XY: 13101 AN XY: 74366

African (AFR) AF: 0.0808 AC: 3356 AN: 41548

American (AMR) AF: 0.208 AC: 3177 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1058 AN: 3472

East Asian (EAS) AF: 0.0841 AC: 435 AN: 5174

South Asian (SAS) AF: 0.212 AC: 1021 AN: 4822

European-Finnish (FIN) AF: 0.186 AC: 1964 AN: 10584

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.227 AC: 15420 AN: 67970

Other (OTH) AF: 0.192 AC: 405 AN: 2110

Alfa AF: 0.127 Hom.: 243

Bravo AF: 0.173

Asia WGS AF: 0.139 AC: 484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.72
PhyloP100		0.30

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10802107;

hg19: chr1-120068932;