rs62057090

chr16-31103589-C-Gchr16-31103589-C-T

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 0.127 in 138,668 control chromosomes in the GnomAD database, including 620 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 0.13 (620 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.204 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: 0.127 AC: 17606 AN: 138592 Hom.: 617 Cov.: 26

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.0945

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.0517

Gnomad FIN AF: 0.0816

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.0959

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.127 AC: 17610 AN: 138668 Hom.: 620 Cov.: 26 AF XY: 0.124 AC XY: 8317 AN XY: 66944

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.0944

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.0526

Gnomad4 FIN AF: 0.0816

Gnomad4 NFE AF: 0.0960

Gnomad4 OTH AF: 0.131

Alfa AF: 0.0826 Hom.: 28

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	3.0
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs62057090; hg19: chr16-31114910;