rs6444175

chr3-186861955-G-A

Variant summary

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

The variant allele was found at a frequency of 0.286 in 151,204 control chromosomes in the GnomAD database, including 6,156 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 0.29 (6156 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43204 AN: 151090 Hom.: 6153 Cov.: 29

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.286 AC: 43217 AN: 151204 Hom.: 6156 Cov.: 29 AF XY: 0.286 AC XY: 21097 AN XY: 73806

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.274

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.287

Alfa AF: 0.274 Hom.: 8373

Bravo AF: 0.284

Asia WGS AF: 0.282 AC: 980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.56
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6444175; hg19: chr3-186579744;