16-67191598-C-T

Variant names:

• chr16-67191598-C-T
• rs3729639

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 0.176 in 151,938 control chromosomes in the GnomAD database, including 4,385 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 0.18 (4385 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921
• Publications: 32 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.432 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: 0.176 AC: 26731 AN: 151820 Hom.: 4375 Cov.: 32

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.0947

Gnomad ASJ AF: 0.0302

Gnomad EAS AF: 0.0206

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0667

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.176 AC: 26781 AN: 151938 Hom.: 4385 Cov.: 32 AF XY: 0.176 AC XY: 13082 AN XY: 74250

African (AFR) AF: 0.438 AC: 18126 AN: 41402

American (AMR) AF: 0.0947 AC: 1446 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0302 AC: 105 AN: 3472

East Asian (EAS) AF: 0.0207 AC: 107 AN: 5176

South Asian (SAS) AF: 0.161 AC: 774 AN: 4812

European-Finnish (FIN) AF: 0.122 AC: 1284 AN: 10518

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0667 AC: 4534 AN: 67978

Other (OTH) AF: 0.132 AC: 278 AN: 2106

Alfa AF: 0.0960 Hom.: 5849

Bravo AF: 0.183

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.7
DANN	Benign	0.61
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs3729639; hg19: chr16-67225501;