chr3-41089171-TTGTC-T

Variant names:

• chr3-41089171-TTGTC-T
• rs2067180
• ENST00000808368.1:n.606+161_606+164delGACA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000808368.1(ENSG00000305067):​n.606+161_606+164delGACA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.45 (16433 hom., cov: 0)
• Consequence: ENSG00000305067 ENST00000808368.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.966
• Publications: 3 publications found

Genes affected

ENSG00000305067 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.541 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
ENSG00000305067	ENST00000808368.1	n.606+161_606+164delGACA		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68283 AN: 151378 Hom.: 16424 Cov.: 0

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.451 AC: 68327 AN: 151496 Hom.: 16433 Cov.: 0 AF XY: 0.444 AC XY: 32830 AN XY: 74012

African (AFR) AF: 0.325 AC: 13438 AN: 41328

American (AMR) AF: 0.421 AC: 6415 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1431 AN: 3464

East Asian (EAS) AF: 0.242 AC: 1247 AN: 5158

South Asian (SAS) AF: 0.276 AC: 1326 AN: 4812

European-Finnish (FIN) AF: 0.574 AC: 5996 AN: 10452

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.546 AC: 36959 AN: 67730

Other (OTH) AF: 0.454 AC: 953 AN: 2100

Alfa AF: 0.488 Hom.: 2275

Bravo AF: 0.439

Asia WGS AF: 0.290 AC: 1010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.97

Splicing

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

Other links and lift over

dbSNP: rs2067180; hg19: chr3-41130662;