ENST00000648816.1:n.218+331A>G

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648816.1. 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
	ENSG00000285703	ENST00000648816.1		n.218+331A>G		intron	N/A
	ENSG00000286652	ENST00000779964.1		n.280-17739T>C		intron	N/A
	ENSG00000286652	ENST00000779965.1		n.276-19310T>C		intron	N/A

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 v4.9

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;