6-27478787-T-C

Variant names:

• chr6-27478787-T-C
• rs7749305
• ENST00000663193.1:n.265+3545T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000663193.1(ENSG00000286652):​n.265+3545T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0954 in 152,256 control chromosomes in the GnomAD database, including 833 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 0.095 (833 hom., cov: 33)
• Consequence: ENSG00000286652 ENST00000663193.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.35
• Publications: 31 publications found

Genes affected

ENSG00000286652 (HGNC:):

TRS-AGA2-2 (HGNC:34637):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000663193.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286652	ENST00000663193.1		n.265+3545T>C		intron	N/A
	ENSG00000286652	ENST00000779964.1		n.279+3545T>C		intron	N/A
	ENSG00000286652	ENST00000779965.1		n.275+3545T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0954 AC: 14521 AN: 152138 Hom.: 834 Cov.: 33

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.0636

Gnomad ASJ AF: 0.0346

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00166

Gnomad FIN AF: 0.0388

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0978

Gnomad OTH AF: 0.0795

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

GnomAD4 genome AF: 0.0954 AC: 14524 AN: 152256 Hom.: 833 Cov.: 33 AF XY: 0.0883 AC XY: 6576 AN XY: 74444

African (AFR) AF: 0.146 AC: 6057 AN: 41528

American (AMR) AF: 0.0635 AC: 972 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0346 AC: 120 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5184

South Asian (SAS) AF: 0.00166 AC: 8 AN: 4826

European-Finnish (FIN) AF: 0.0388 AC: 412 AN: 10612

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0977 AC: 6647 AN: 68022

Other (OTH) AF: 0.0796 AC: 168 AN: 2110

Alfa AF: 0.0976 Hom.: 1597

Bravo AF: 0.100

Asia WGS AF: 0.0130 AC: 46 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	0.28
DANN	Benign	0.33
PhyloP100		-3.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7749305;

hg19: chr6-27446566;