rs10883617

Variant names:

• chr10-101353278-T-C
• rs10883617
• ENST00000727786.1:n.1156T>C

Variant summary

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

The ENST00000727786.1(ENSG00000225208):​n.1156T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,106 control chromosomes in the GnomAD database, including 6,540 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 0.28 (6540 hom., cov: 32)
• Consequence: ENSG00000225208 ENST00000727786.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600
• Publications: 9 publications found

Genes affected

ENSG00000225208 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.353 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
ENSG00000225208	ENST00000727786.1	n.1156T>C		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000225208	ENST00000442188.2	n.*186T>C		downstream_gene_variant		3
ENSG00000225208	ENST00000727787.1	n.*142T>C		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42353 AN: 151988 Hom.: 6534 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.279 AC: 42378 AN: 152106 Hom.: 6540 Cov.: 32 AF XY: 0.275 AC XY: 20481 AN XY: 74352

African (AFR) AF: 0.161 AC: 6672 AN: 41504

American (AMR) AF: 0.265 AC: 4055 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1331 AN: 3466

East Asian (EAS) AF: 0.138 AC: 713 AN: 5184

South Asian (SAS) AF: 0.216 AC: 1042 AN: 4820

European-Finnish (FIN) AF: 0.310 AC: 3282 AN: 10574

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.356 AC: 24217 AN: 67970

Other (OTH) AF: 0.284 AC: 599 AN: 2108

Alfa AF: 0.322 Hom.: 17818

Bravo AF: 0.270

Asia WGS AF: 0.174 AC: 606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.7
DANN	Benign	0.55
PhyloP100		-0.0060

Splicing

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

Other links and lift over

dbSNP: rs10883617; hg19: chr10-103113035;