rs6444175

Variant names:

• chr3-186861955-G-A
• rs6444175

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 34 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.304 AC: 12486 AN: 41122

American (AMR) AF: 0.300 AC: 4553 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1069 AN: 3464

East Asian (EAS) AF: 0.274 AC: 1407 AN: 5144

South Asian (SAS) AF: 0.247 AC: 1186 AN: 4806

European-Finnish (FIN) AF: 0.315 AC: 3256 AN: 10336

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.270 AC: 18350 AN: 67886

Other (OTH) AF: 0.287 AC: 600 AN: 2088

Alfa AF: 0.274 Hom.: 11615

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
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs6444175; hg19: chr3-186579744;