6-166993145-G-C

Variant names:

• chr6-166993145-G-C
• rs415890
• ENST00000444102.1:n.148+5773C>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 49 publications found

Genes affected

ENSG00000227598 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000444102.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000227598	ENST00000444102.1	TSL:5	n.148+5773C>G		intron	N/A
	ENSG00000227598	ENST00000832409.1		n.166+5773C>G		intron	N/A

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

African (AFR) AF: 0.268 AC: 11112 AN: 41472

American (AMR) AF: 0.388 AC: 5919 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1635 AN: 3470

East Asian (EAS) AF: 0.379 AC: 1962 AN: 5170

South Asian (SAS) AF: 0.305 AC: 1469 AN: 4820

European-Finnish (FIN) AF: 0.466 AC: 4915 AN: 10548

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.532 AC: 36181 AN: 67954

Other (OTH) AF: 0.411 AC: 867 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.8
DANN	Benign	0.82
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs415890; hg19: chr6-167406633;