rs1982396

Variant names:

• chr16-60228514-C-T
• rs1982396

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 0.289 in 152,000 control chromosomes in the GnomAD database, including 6,507 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 0.29 (6507 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.548
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 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: 0.289 AC: 43892 AN: 151882 Hom.: 6500 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.289 AC: 43932 AN: 152000 Hom.: 6507 Cov.: 32 AF XY: 0.283 AC XY: 21040 AN XY: 74254

African (AFR) AF: 0.311 AC: 12902 AN: 41442

American (AMR) AF: 0.235 AC: 3586 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 843 AN: 3468

East Asian (EAS) AF: 0.210 AC: 1076 AN: 5136

South Asian (SAS) AF: 0.295 AC: 1422 AN: 4814

European-Finnish (FIN) AF: 0.241 AC: 2541 AN: 10548

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20695 AN: 67998

Other (OTH) AF: 0.250 AC: 526 AN: 2108

Alfa AF: 0.297 Hom.: 1396

Bravo AF: 0.288

Asia WGS AF: 0.248 AC: 862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.20
DANN	Benign	0.47
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs1982396; hg19: chr16-60262418;