3-51738331-A-G

Variant names:

• chr3-51738331-A-G
• rs6445959

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 0.242 in 151,750 control chromosomes in the GnomAD database, including 5,455 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 0.24 (5455 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0940
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36715 AN: 151632 Hom.: 5431 Cov.: 30

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.242 AC: 36782 AN: 151750 Hom.: 5455 Cov.: 30 AF XY: 0.245 AC XY: 18171 AN XY: 74162

African (AFR) AF: 0.368 AC: 15223 AN: 41344

American (AMR) AF: 0.369 AC: 5624 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 495 AN: 3468

East Asian (EAS) AF: 0.443 AC: 2254 AN: 5084

South Asian (SAS) AF: 0.178 AC: 853 AN: 4802

European-Finnish (FIN) AF: 0.179 AC: 1888 AN: 10564

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9784 AN: 67938

Other (OTH) AF: 0.212 AC: 447 AN: 2108

Alfa AF: 0.181 Hom.: 14060

Bravo AF: 0.267

Asia WGS AF: 0.306 AC: 1065 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.9
DANN	Benign	0.33
PhyloP100		0.094

Splicing

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

Other links and lift over

dbSNP: rs6445959; hg19: chr3-51772347;