chr16-74709838-C-T

Variant names:

• chr16-74709838-C-T
• rs7187229

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 0.793 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.788 AC: 32704 AN: 41512

American (AMR) AF: 0.776 AC: 11860 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.833 AC: 2889 AN: 3470

East Asian (EAS) AF: 0.598 AC: 3092 AN: 5170

South Asian (SAS) AF: 0.702 AC: 3384 AN: 4820

European-Finnish (FIN) AF: 0.831 AC: 8801 AN: 10592

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.814 AC: 55346 AN: 67984

Other (OTH) AF: 0.807 AC: 1707 AN: 2116

Alfa AF: 0.807 Hom.: 227852

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
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs7187229; hg19: chr16-74743736;