chr16-20331769-T-C

Position:

• chr16-20331769-T-C

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 0.775 in 152,208 control chromosomes in the GnomAD database, including 46,951 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 0.78 (46951 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 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: 0.775 AC: 117897 AN: 152090 Hom.: 46891 Cov.: 33

Gnomad AFR AF: 0.943

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.992

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.763

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

GnomAD4 genome AF: 0.775 AC: 118011 AN: 152208 Hom.: 46951 Cov.: 33 AF XY: 0.773 AC XY: 57521 AN XY: 74402

Gnomad4 AFR AF: 0.943

Gnomad4 AMR AF: 0.685

Gnomad4 ASJ AF: 0.762

Gnomad4 EAS AF: 0.992

Gnomad4 SAS AF: 0.849

Gnomad4 FIN AF: 0.675

Gnomad4 NFE AF: 0.690

Gnomad4 OTH AF: 0.766

Alfa AF: 0.699 Hom.: 49268

Bravo AF: 0.784

Asia WGS AF: 0.914 AC: 3181 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	0.31
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4238595; hg19: chr16-20343091;