6-139547773-T-C

Variant names:

• chr6-139547773-T-C
• rs10484821
• ENST00000647815.1:n.135-58486T>C

Variant summary

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

The ENST00000647815.1(ENSG00000226571):​n.135-58486T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,228 control chromosomes in the GnomAD database, including 2,062 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 0.15 (2062 hom., cov: 33)
• Consequence: ENSG00000226571 ENST00000647815.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590
• Publications: 7 publications found

Genes affected

ENSG00000226571 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647815.1. 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
	ENSG00000226571	ENST00000647815.1		n.135-58486T>C		intron	N/A
	ENSG00000226571	ENST00000648888.1		n.98+13357T>C		intron	N/A
	ENSG00000226571	ENST00000775599.1		n.343-5671T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22598 AN: 152110 Hom.: 2064 Cov.: 33

Gnomad AFR AF: 0.0589

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.148 AC: 22586 AN: 152228 Hom.: 2062 Cov.: 33 AF XY: 0.151 AC XY: 11211 AN XY: 74414

African (AFR) AF: 0.0588 AC: 2441 AN: 41546

American (AMR) AF: 0.112 AC: 1713 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 387 AN: 3470

East Asian (EAS) AF: 0.317 AC: 1639 AN: 5172

South Asian (SAS) AF: 0.145 AC: 702 AN: 4830

European-Finnish (FIN) AF: 0.246 AC: 2604 AN: 10592

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12574 AN: 68016

Other (OTH) AF: 0.123 AC: 259 AN: 2110

Alfa AF: 0.150 Hom.: 1179

Bravo AF: 0.135

Asia WGS AF: 0.180 AC: 625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.55
DANN	Benign	0.43
PhyloP100		-0.059

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: rs10484821;

hg19: chr6-139868910;