rs10802112

Variant names:

• chr1-119548811-T-C
• rs10802112
• ENST00000632456.2:n.242+6489A>G

Variant summary

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

The ENST00000632456.2(ENSG00000293080):​n.242+6489A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 152,014 control chromosomes in the GnomAD database, including 3,841 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 0.22 (3841 hom., cov: 32)
• Consequence: ENSG00000293080 ENST00000632456.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 10 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000632456.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293080	ENST00000632456.2	TSL:6	n.242+6489A>G		intron	N/A
	ENSG00000293080	ENST00000756941.1		n.218+6489A>G		intron	N/A
	ENSG00000293080	ENST00000756942.1		n.258+6489A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33586 AN: 151896 Hom.: 3838 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.221 AC: 33603 AN: 152014 Hom.: 3841 Cov.: 32 AF XY: 0.221 AC XY: 16409 AN XY: 74308

African (AFR) AF: 0.163 AC: 6775 AN: 41466

American (AMR) AF: 0.226 AC: 3460 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1110 AN: 3470

East Asian (EAS) AF: 0.217 AC: 1119 AN: 5156

South Asian (SAS) AF: 0.358 AC: 1721 AN: 4808

European-Finnish (FIN) AF: 0.192 AC: 2026 AN: 10560

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.246 AC: 16687 AN: 67960

Other (OTH) AF: 0.233 AC: 492 AN: 2112

Alfa AF: 0.241 Hom.: 12869

Bravo AF: 0.216

Asia WGS AF: 0.266 AC: 925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.077
DANN	Benign	0.64
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10802112; hg19: chr1-120091434;