rs6444210

Variant names:

• chr3-187192871-T-C
• rs6444210

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 0.48 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
• Publications: 2 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.295 AC: 12233 AN: 41482

American (AMR) AF: 0.551 AC: 8409 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1770 AN: 3470

East Asian (EAS) AF: 0.573 AC: 2957 AN: 5164

South Asian (SAS) AF: 0.522 AC: 2516 AN: 4820

European-Finnish (FIN) AF: 0.509 AC: 5374 AN: 10552

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.560 AC: 38079 AN: 67976

Other (OTH) AF: 0.509 AC: 1074 AN: 2108

Alfa AF: 0.534 Hom.: 68402

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
PhyloP100		-3.8

Splicing

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

Other links and lift over

dbSNP: rs6444210; hg19: chr3-186910659;