rs10456051

Variant names:

• chr6-27495657-T-C
• rs10456051
• ENST00000648816.1:n.218+331A>G

Variant summary

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

The ENST00000648816.1(ENSG00000285703):​n.218+331A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0488 in 152,330 control chromosomes in the GnomAD database, including 262 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 0.049 (262 hom., cov: 32)
• Consequence: ENSG00000285703 ENST00000648816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30
• Publications: 5 publications found

Genes affected

ENSG00000285703 (HGNC:):

TRS-AGA2-3 (HGNC:16293):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRS-AGA2-3	unassigned_transcript_1015	c.-157T>C		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285703	ENST00000648816.1	n.218+331A>G		intron_variant	Intron 2 of 3
ENSG00000286652	ENST00000779964.1	n.280-17739T>C		intron_variant	Intron 2 of 3
ENSG00000286652	ENST00000779965.1	n.276-19310T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0488 AC: 7435 AN: 152212 Hom.: 262 Cov.: 32

Gnomad AFR AF: 0.0124

Gnomad AMI AF: 0.0879

Gnomad AMR AF: 0.0329

Gnomad ASJ AF: 0.0222

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.0211

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0731

Gnomad OTH AF: 0.0349

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

GnomAD4 genome AF: 0.0488 AC: 7435 AN: 152330 Hom.: 262 Cov.: 32 AF XY: 0.0492 AC XY: 3662 AN XY: 74476

African (AFR) AF: 0.0124 AC: 516 AN: 41596

American (AMR) AF: 0.0329 AC: 504 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0222 AC: 77 AN: 3472

East Asian (EAS) AF: 0.00290 AC: 15 AN: 5180

South Asian (SAS) AF: 0.0213 AC: 103 AN: 4826

European-Finnish (FIN) AF: 0.103 AC: 1095 AN: 10608

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0730 AC: 4969 AN: 68026

Other (OTH) AF: 0.0345 AC: 73 AN: 2114

Alfa AF: 0.0610 Hom.: 625

Bravo AF: 0.0431

Asia WGS AF: 0.0150 AC: 51 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	11
DANN	Benign	0.41
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs10456051; hg19: chr6-27463436;