16-60105237-T-G

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 0.948 in 152,306 control chromosomes in the GnomAD database, including 68,449 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 0.95 (68449 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.503

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.979 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: 0.948 AC: 144200 AN: 152188 Hom.: 68388 Cov.: 33

Gnomad AFR AF: 0.987

Gnomad AMI AF: 0.953

Gnomad AMR AF: 0.945

Gnomad ASJ AF: 0.901

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.986

Gnomad FIN AF: 0.943

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.921

Gnomad OTH AF: 0.934

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

GnomAD4 genome AF: 0.948 AC: 144320 AN: 152306 Hom.: 68449 Cov.: 33 AF XY: 0.949 AC XY: 70673 AN XY: 74450

Gnomad4 AFR AF: 0.987

Gnomad4 AMR AF: 0.945

Gnomad4 ASJ AF: 0.901

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.986

Gnomad4 FIN AF: 0.943

Gnomad4 NFE AF: 0.921

Gnomad4 OTH AF: 0.934

Alfa AF: 0.929 Hom.: 29393

Bravo AF: 0.947

Asia WGS AF: 0.990 AC: 3441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	5.3
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1364194; hg19: chr16-60139141;