6-166993145-G-C

Position:

• chr6-166993145-G-C

Variant summary

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

The ENST00000444102.1(ENSG00000227598):​n.148+5773C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 152,018 control chromosomes in the GnomAD database, including 14,717 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 0.42 (14717 hom., cov: 32)
• Consequence: ENSG00000227598 ENST00000444102.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.636

Genes affected

ENSG00000227598 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000227598	ENST00000444102.1	n.148+5773C>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64581 AN: 151900 Hom.: 14716 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.425 AC: 64593 AN: 152018 Hom.: 14717 Cov.: 32 AF XY: 0.420 AC XY: 31163 AN XY: 74276

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.379

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.466

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.411

Alfa AF: 0.353 Hom.: 1076

Bravo AF: 0.410

Asia WGS AF: 0.336 AC: 1171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.8
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs415890; hg19: chr6-167406633;