3-62897705-C-T

Variant names:

• chr3-62897705-C-T
• rs1992192

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 0.337 in 151,978 control chromosomes in the GnomAD database, including 9,442 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 0.34 (9442 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.300

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.487 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: 0.336 AC: 51061 AN: 151860 Hom.: 9418 Cov.: 32

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.337 AC: 51143 AN: 151978 Hom.: 9442 Cov.: 32 AF XY: 0.339 AC XY: 25162 AN XY: 74304

Gnomad4 AFR AF: 0.492

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.387

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.308

Alfa AF: 0.257 Hom.: 7245

Bravo AF: 0.355

Asia WGS AF: 0.311 AC: 1081 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.6
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1992192; hg19: chr3-62883380;