16-27373410-T-G

Variant names:

• chr16-27373410-T-G
• rs4787426

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 0.18 in 152,152 control chromosomes in the GnomAD database, including 3,140 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 (3140 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.321 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: 0.180 AC: 27359 AN: 152034 Hom.: 3124 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.0891

Gnomad SAS AF: 0.0645

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.180 AC: 27427 AN: 152152 Hom.: 3140 Cov.: 32 AF XY: 0.175 AC XY: 12998 AN XY: 74384

African (AFR) AF: 0.325 AC: 13495 AN: 41472

American (AMR) AF: 0.157 AC: 2393 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 422 AN: 3468

East Asian (EAS) AF: 0.0893 AC: 463 AN: 5186

South Asian (SAS) AF: 0.0645 AC: 311 AN: 4820

European-Finnish (FIN) AF: 0.125 AC: 1323 AN: 10592

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8513 AN: 68020

Other (OTH) AF: 0.152 AC: 322 AN: 2112

Alfa AF: 0.138 Hom.: 3222

Bravo AF: 0.190

Asia WGS AF: 0.107 AC: 370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.7
DANN	Benign	0.37
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs4787426; hg19: chr16-27384731;