rs2042360

Variant names:

• chr16-64123913-T-C
• rs2042360

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 0.178 in 152,128 control chromosomes in the GnomAD database, including 2,879 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 0.18 (2879 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.332 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: 0.178 AC: 27110 AN: 152010 Hom.: 2871 Cov.: 32

Gnomad AFR AF: 0.0693

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.178 AC: 27133 AN: 152128 Hom.: 2879 Cov.: 32 AF XY: 0.180 AC XY: 13422 AN XY: 74364

Gnomad4 AFR AF: 0.0693

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.214

Gnomad4 EAS AF: 0.257

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.210

Alfa AF: 0.214 Hom.: 2212

Bravo AF: 0.175

Asia WGS AF: 0.302 AC: 1047 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.86
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2042360; hg19: chr16-64157817;