chr16-2203772-A-G

Position:

• chr16-2203772-A-G

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 0.416 in 152,074 control chromosomes in the GnomAD database, including 15,899 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 0.42 (15899 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.568 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: 0.416 AC: 63265 AN: 151956 Hom.: 15902 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.416 AC: 63278 AN: 152074 Hom.: 15899 Cov.: 32 AF XY: 0.422 AC XY: 31382 AN XY: 74342

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.585

Gnomad4 SAS AF: 0.526

Gnomad4 FIN AF: 0.571

Gnomad4 NFE AF: 0.537

Gnomad4 OTH AF: 0.417

Alfa AF: 0.496 Hom.: 19229

Bravo AF: 0.394

Asia WGS AF: 0.521 AC: 1807 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.3
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs26865; hg19: chr16-2253773;