6-139547773-T-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000226571 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378024	XR_943068.3	n.*83T>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226571	ENST00000647815.1	n.135-58486T>C		intron_variant	Intron 1 of 2
ENSG00000226571	ENST00000648888.1	n.98+13357T>C		intron_variant	Intron 1 of 11

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

Gnomad4 AFR AF: 0.0588

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.123

Alfa AF: 0.149 Hom.: 1058

Bravo AF: 0.135

Asia WGS AF: 0.180 AC: 625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484821; hg19: chr6-139868910;