rs6444210

chr3-187192871-T-C

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 0.48 in 152,052 control chromosomes in the GnomAD database, including 18,540 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 0.48 (18540 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.82

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.555 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: 0.481 AC: 73007 AN: 151934 Hom.: 18549 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.513

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

GnomAD4 genome AF: 0.480 AC: 73008 AN: 152052 Hom.: 18540 Cov.: 32 AF XY: 0.482 AC XY: 35814 AN XY: 74330

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.551

Gnomad4 ASJ AF: 0.510

Gnomad4 EAS AF: 0.573

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.509

Gnomad4 NFE AF: 0.560

Gnomad4 OTH AF: 0.509

Alfa AF: 0.550 Hom.: 46742

Bravo AF: 0.477

Asia WGS AF: 0.495 AC: 1719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.012
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6444210; hg19: chr3-186910659;