rs1344485

Positions:

• chr16-52878420-A-G
• chr16-52878420-A-T

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 0.344 in 152,142 control chromosomes in the GnomAD database, including 9,673 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 0.34 (9673 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.383

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.58 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: 0.344 AC: 52367 AN: 152024 Hom.: 9666 Cov.: 33

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.344 AC: 52391 AN: 152142 Hom.: 9673 Cov.: 33 AF XY: 0.346 AC XY: 25726 AN XY: 74362

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.598

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.376

Gnomad4 OTH AF: 0.356

Alfa AF: 0.375 Hom.: 6421

Bravo AF: 0.349

Asia WGS AF: 0.442 AC: 1537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.25
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1344485; hg19: chr16-52912332;