16-74709838-C-T

Position:

• chr16-74709838-C-T

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 0.793 in 152,146 control chromosomes in the GnomAD database, including 47,975 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 0.79 (47975 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147

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 (NFE) allele frequency at 95% confidence interval = 0.808 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: 0.793 AC: 120583 AN: 152028 Hom.: 47925 Cov.: 33

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.703

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.808

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

GnomAD4 genome AF: 0.793 AC: 120692 AN: 152146 Hom.: 47975 Cov.: 33 AF XY: 0.790 AC XY: 58787 AN XY: 74380

Gnomad4 AFR AF: 0.788

Gnomad4 AMR AF: 0.776

Gnomad4 ASJ AF: 0.833

Gnomad4 EAS AF: 0.598

Gnomad4 SAS AF: 0.702

Gnomad4 FIN AF: 0.831

Gnomad4 NFE AF: 0.814

Gnomad4 OTH AF: 0.807

Alfa AF: 0.811 Hom.: 105965

Bravo AF: 0.790

Asia WGS AF: 0.671 AC: 2334 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	3.8
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7187229; hg19: chr16-74743736;