6-48567193-A-T

Variant names:

• chr6-48567193-A-T
• rs2052800
• ENST00000730502.1:n.282+27912A>T

Variant summary

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

The ENST00000730502.1(ENSG00000295504):​n.282+27912A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 152,030 control chromosomes in the GnomAD database, including 12,097 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 0.36 (12097 hom., cov: 32)
• Consequence: ENSG00000295504 ENST00000730502.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24
• Publications: 0 publications found

Genes affected

ENSG00000295504 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000730502.1. 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
	ENSG00000295504	ENST00000730502.1		n.282+27912A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55167 AN: 151914 Hom.: 12059 Cov.: 32

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.364 AC: 55268 AN: 152030 Hom.: 12097 Cov.: 32 AF XY: 0.366 AC XY: 27236 AN XY: 74334

African (AFR) AF: 0.531 AC: 22007 AN: 41430

American (AMR) AF: 0.434 AC: 6625 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 741 AN: 3470

East Asian (EAS) AF: 0.784 AC: 4054 AN: 5170

South Asian (SAS) AF: 0.504 AC: 2429 AN: 4822

European-Finnish (FIN) AF: 0.220 AC: 2325 AN: 10586

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16101 AN: 67960

Other (OTH) AF: 0.341 AC: 720 AN: 2110

Alfa AF: 0.166 Hom.: 315

Bravo AF: 0.389

Asia WGS AF: 0.604 AC: 2099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.22
DANN	Benign	0.46
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs2052800; hg19: chr6-48534929;