10-122529208-G-A

Variant names:

• chr10-122529208-G-A
• rs7902878
• ENST00000751010.1:n.*235C>T

Variant summary

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

The ENST00000751010.1(ENSG00000297803):​n.*235C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 151,676 control chromosomes in the GnomAD database, including 5,042 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 (5042 hom., cov: 31)
• Consequence: ENSG00000297803 ENST00000751010.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.697
• Publications: 2 publications found

Genes affected

ENSG00000297803 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.299 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
ENSG00000297803	ENST00000751010.1	n.*235C>T		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37078 AN: 151556 Hom.: 5040 Cov.: 31

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.244 AC: 37075 AN: 151676 Hom.: 5042 Cov.: 31 AF XY: 0.246 AC XY: 18193 AN XY: 74044

African (AFR) AF: 0.134 AC: 5559 AN: 41388

American (AMR) AF: 0.223 AC: 3405 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 817 AN: 3466

East Asian (EAS) AF: 0.205 AC: 1047 AN: 5102

South Asian (SAS) AF: 0.189 AC: 902 AN: 4776

European-Finnish (FIN) AF: 0.373 AC: 3908 AN: 10472

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20554 AN: 67914

Other (OTH) AF: 0.234 AC: 494 AN: 2108

Alfa AF: 0.276 Hom.: 25057

Bravo AF: 0.226

Asia WGS AF: 0.194 AC: 675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.52
DANN	Benign	0.26
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs7902878; hg19: chr10-124288724;