16-69529987-C-T

Variant names:

• chr16-69529987-C-T
• rs7193778

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 0.898 in 152,252 control chromosomes in the GnomAD database, including 61,596 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 0.90 (61596 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.966 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: 0.898 AC: 136583 AN: 152134 Hom.: 61538 Cov.: 32

Gnomad AFR AF: 0.974

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.877

Gnomad ASJ AF: 0.913

Gnomad EAS AF: 0.940

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.860

Gnomad OTH AF: 0.891

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

GnomAD4 genome AF: 0.898 AC: 136699 AN: 152252 Hom.: 61596 Cov.: 32 AF XY: 0.899 AC XY: 66942 AN XY: 74432

Gnomad4 AFR AF: 0.974

Gnomad4 AMR AF: 0.877

Gnomad4 ASJ AF: 0.913

Gnomad4 EAS AF: 0.940

Gnomad4 SAS AF: 0.872

Gnomad4 FIN AF: 0.868

Gnomad4 NFE AF: 0.860

Gnomad4 OTH AF: 0.892

Alfa AF: 0.880 Hom.: 9856

Bravo AF: 0.900

Asia WGS AF: 0.911 AC: 3170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.11
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7193778; hg19: chr16-69563890;