rs62057090

Variant names:

• chr16-31103589-C-G
• rs62057090

Your query was ambiguous. Multiple possible variants found:

• chr16-31103589-C-G
• chr16-31103589-C-T

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 0.127 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
• Publications: 3 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.208 AC: 7882 AN: 37900

American (AMR) AF: 0.0944 AC: 1325 AN: 14038

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 406 AN: 3220

East Asian (EAS) AF: 0.139 AC: 579 AN: 4158

South Asian (SAS) AF: 0.0526 AC: 234 AN: 4448

European-Finnish (FIN) AF: 0.0816 AC: 730 AN: 8950

Middle Eastern (MID) AF: 0.151 AC: 41 AN: 272

European-Non Finnish (NFE) AF: 0.0960 AC: 6041 AN: 62952

Other (OTH) AF: 0.131 AC: 247 AN: 1886

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

Other links and lift over

dbSNP: rs62057090; hg19: chr16-31114910;