16-60078907-T-G

Variant names:

• chr16-60078907-T-G
• rs2911242

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 0.752 in 151,764 control chromosomes in the GnomAD database, including 43,674 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 0.75 (43674 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.943 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: 0.752 AC: 114014 AN: 151646 Hom.: 43610 Cov.: 30

Gnomad AFR AF: 0.880

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.755

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.966

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.752 AC: 114140 AN: 151764 Hom.: 43674 Cov.: 30 AF XY: 0.754 AC XY: 55913 AN XY: 74134

Gnomad4 AFR AF: 0.881

Gnomad4 AMR AF: 0.755

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.966

Gnomad4 SAS AF: 0.733

Gnomad4 FIN AF: 0.708

Gnomad4 NFE AF: 0.673

Gnomad4 OTH AF: 0.730

Alfa AF: 0.609 Hom.: 1612

Bravo AF: 0.763

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.62
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2911242; hg19: chr16-60112811;