16-64793581-T-G

Variant names:

• chr16-64793581-T-G
• rs1424003

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.0932 in 152,060 control chromosomes in the GnomAD database, including 864 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 0.093 (864 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.96

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.15).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.138 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: 0.0932 AC: 14166 AN: 151942 Hom.: 863 Cov.: 32

Gnomad AFR AF: 0.0236

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.0809

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.000775

Gnomad SAS AF: 0.0799

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.0932 AC: 14168 AN: 152060 Hom.: 864 Cov.: 32 AF XY: 0.0911 AC XY: 6772 AN XY: 74340

Gnomad4 AFR AF: 0.0235

Gnomad4 AMR AF: 0.0807

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.000972

Gnomad4 SAS AF: 0.0806

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0719 Hom.: 101

Bravo AF: 0.0906

Asia WGS AF: 0.0340 AC: 118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.15
CADD	Benign	23
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1424003; hg19: chr16-64827484;