16-79913741-C-T

Variant names:

• chr16-79913741-C-T
• rs7189172

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 0.496 in 151,634 control chromosomes in the GnomAD database, including 22,924 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 0.50 (22924 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290

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 (AFR) allele frequency at 95% confidence interval = 0.856 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: 0.495 AC: 75010 AN: 151518 Hom.: 22845 Cov.: 31

Gnomad AFR AF: 0.863

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.496 AC: 75153 AN: 151634 Hom.: 22924 Cov.: 31 AF XY: 0.499 AC XY: 36931 AN XY: 74050

Gnomad4 AFR AF: 0.863

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.515

Gnomad4 SAS AF: 0.414

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.312

Gnomad4 OTH AF: 0.467

Alfa AF: 0.391 Hom.: 3381

Bravo AF: 0.515

Asia WGS AF: 0.525 AC: 1821 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	0.76
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7189172; hg19: chr16-79947638;