6-105740943-C-T

Variant names:

• chr6-105740943-C-T
• rs6568401
• ENST00000644129.1:n.282-61452G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000644129.1(ENSG00000284999):​n.282-61452G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 151,924 control chromosomes in the GnomAD database, including 36,470 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 0.69 (36470 hom., cov: 33)
• Consequence: ENSG00000284999 ENST00000644129.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.556

Genes affected

ENSG00000284999 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000284999	ENST00000644129.1	n.282-61452G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104651 AN: 151806 Hom.: 36449 Cov.: 33

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.710

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.723

Gnomad OTH AF: 0.699

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

GnomAD4 genome AF: 0.689 AC: 104720 AN: 151924 Hom.: 36470 Cov.: 33 AF XY: 0.689 AC XY: 51149 AN XY: 74242

Gnomad4 AFR AF: 0.599

Gnomad4 AMR AF: 0.788

Gnomad4 ASJ AF: 0.770

Gnomad4 EAS AF: 0.637

Gnomad4 SAS AF: 0.811

Gnomad4 FIN AF: 0.624

Gnomad4 NFE AF: 0.723

Gnomad4 OTH AF: 0.702

Alfa AF: 0.711 Hom.: 14091

Bravo AF: 0.692

Asia WGS AF: 0.746 AC: 2596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	7.5
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: rs6568401; hg19: chr6-106188818;