16-62066307-T-C

Position:

• chr16-62066307-T-C

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 0.092 in 152,156 control chromosomes in the GnomAD database, including 1,604 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 0.092 (1604 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.27 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: 0.0915 AC: 13919 AN: 152038 Hom.: 1584 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.0387

Gnomad ASJ AF: 0.0112

Gnomad EAS AF: 0.0400

Gnomad SAS AF: 0.0360

Gnomad FIN AF: 0.0181

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0178

Gnomad OTH AF: 0.0674

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

GnomAD4 genome AF: 0.0920 AC: 13991 AN: 152156 Hom.: 1604 Cov.: 32 AF XY: 0.0900 AC XY: 6696 AN XY: 74414

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.0386

Gnomad4 ASJ AF: 0.0112

Gnomad4 EAS AF: 0.0403

Gnomad4 SAS AF: 0.0354

Gnomad4 FIN AF: 0.0181

Gnomad4 NFE AF: 0.0178

Gnomad4 OTH AF: 0.0662

Alfa AF: 0.0307 Hom.: 394

Bravo AF: 0.102

Asia WGS AF: 0.0580 AC: 202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.46
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8050940; hg19: chr16-62100211;