16-29738583-G-T

Variant names:

• chr16-29738583-G-T
• rs7193756

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 0.263 in 151,986 control chromosomes in the GnomAD database, including 6,844 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 0.26 (6844 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.245
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.493 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: 0.263 AC: 39943 AN: 151868 Hom.: 6824 Cov.: 32

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.263 AC: 39998 AN: 151986 Hom.: 6844 Cov.: 32 AF XY: 0.260 AC XY: 19316 AN XY: 74304

African (AFR) AF: 0.498 AC: 20640 AN: 41426

American (AMR) AF: 0.157 AC: 2397 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 553 AN: 3468

East Asian (EAS) AF: 0.127 AC: 655 AN: 5172

South Asian (SAS) AF: 0.171 AC: 823 AN: 4822

European-Finnish (FIN) AF: 0.190 AC: 2005 AN: 10546

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12134 AN: 67978

Other (OTH) AF: 0.206 AC: 435 AN: 2110

Alfa AF: 0.210 Hom.: 5725

Bravo AF: 0.270

Asia WGS AF: 0.129 AC: 447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.82
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs7193756; hg19: chr16-29749904;