rs1344485

Variant names:

• chr16-52878420-A-G
• rs1344485

Your query was ambiguous. Multiple possible variants found:

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

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 0.344 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.204 AC: 8462 AN: 41524

American (AMR) AF: 0.439 AC: 6708 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1193 AN: 3472

East Asian (EAS) AF: 0.598 AC: 3091 AN: 5172

South Asian (SAS) AF: 0.405 AC: 1952 AN: 4824

European-Finnish (FIN) AF: 0.402 AC: 4245 AN: 10550

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25594 AN: 67992

Other (OTH) AF: 0.356 AC: 753 AN: 2114

Alfa AF: 0.375 Hom.: 6905

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
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs1344485; hg19: chr16-52912332;