chr3-41089171-TTGTC-T

Position:

• chr3-41089171-TTGTC-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.45 (16433 hom., cov: 0)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.966

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.41089172_41089175delTGTC		intergenic_region

Ensembl

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

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

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.574

Gnomad4 NFE AF: 0.546

Gnomad4 OTH AF: 0.454

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2067180; hg19: chr3-41130662;