10-8983232-T-C

Variant names:

• chr10-8983232-T-C
• rs1663689
• ENST00000798219.1:n.*57A>G

Variant summary

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

The ENST00000798219.1(ENSG00000303941):​n.*57A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 152,034 control chromosomes in the GnomAD database, including 5,126 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 0.25 (5126 hom., cov: 31)
• Consequence: ENSG00000303941 ENST00000798219.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.113
• Publications: 11 publications found

Genes affected

ENSG00000303941 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.407 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
ENSG00000303941	ENST00000798219.1	n.*57A>G		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38159 AN: 151916 Hom.: 5110 Cov.: 31

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.251 AC: 38217 AN: 152034 Hom.: 5126 Cov.: 31 AF XY: 0.251 AC XY: 18629 AN XY: 74316

African (AFR) AF: 0.306 AC: 12701 AN: 41464

American (AMR) AF: 0.271 AC: 4142 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 921 AN: 3470

East Asian (EAS) AF: 0.421 AC: 2168 AN: 5146

South Asian (SAS) AF: 0.332 AC: 1600 AN: 4814

European-Finnish (FIN) AF: 0.144 AC: 1528 AN: 10578

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14255 AN: 67986

Other (OTH) AF: 0.245 AC: 518 AN: 2114

Alfa AF: 0.233 Hom.: 738

Bravo AF: 0.261

Asia WGS AF: 0.377 AC: 1312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.71
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs1663689; hg19: chr10-9025195;