rs1482258

Variant names:

• chr16-59477187-C-A
• rs1482258

Your query was ambiguous. Multiple possible variants found:

• chr16-59477187-C-A
• chr16-59477187-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 0.573 in 151,698 control chromosomes in the GnomAD database, including 25,675 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 0.57 (25675 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.253
• 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 = 0.701 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: 0.573 AC: 86824 AN: 151580 Hom.: 25624 Cov.: 30

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.573 AC: 86939 AN: 151698 Hom.: 25675 Cov.: 30 AF XY: 0.568 AC XY: 42085 AN XY: 74092

African (AFR) AF: 0.708 AC: 29302 AN: 41396

American (AMR) AF: 0.624 AC: 9489 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2090 AN: 3466

East Asian (EAS) AF: 0.431 AC: 2205 AN: 5116

South Asian (SAS) AF: 0.552 AC: 2658 AN: 4812

European-Finnish (FIN) AF: 0.389 AC: 4080 AN: 10490

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.517 AC: 35124 AN: 67904

Other (OTH) AF: 0.598 AC: 1256 AN: 2100

Alfa AF: 0.551 Hom.: 3135

Bravo AF: 0.592

Asia WGS AF: 0.560 AC: 1946 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.80
DANN	Benign	0.57
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs1482258; hg19: chr16-59511091;