16-60105237-T-G

Variant names:

• chr16-60105237-T-G
• rs1364194

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 0.948 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.987 AC: 41070 AN: 41590

American (AMR) AF: 0.945 AC: 14445 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.901 AC: 3129 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5170 AN: 5172

South Asian (SAS) AF: 0.986 AC: 4758 AN: 4824

European-Finnish (FIN) AF: 0.943 AC: 9991 AN: 10600

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.921 AC: 62644 AN: 68034

Other (OTH) AF: 0.934 AC: 1977 AN: 2116

Alfa AF: 0.937 Hom.: 39086

Bravo AF: 0.947

Asia WGS AF: 0.990 AC: 3441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.3
DANN	Benign	0.33
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs1364194; hg19: chr16-60139141;