rs4075052

Variant names:

• chr16-31336912-A-C
• rs4075052

Your query was ambiguous. Multiple possible variants found:

• chr16-31336912-A-C
• chr16-31336912-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 0.727 in 152,186 control chromosomes in the GnomAD database, including 41,319 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 0.73 (41319 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.892 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: 0.727 AC: 110606 AN: 152068 Hom.: 41284 Cov.: 32

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.866

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.739

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

GnomAD4 genome AF: 0.727 AC: 110692 AN: 152186 Hom.: 41319 Cov.: 32 AF XY: 0.719 AC XY: 53493 AN XY: 74398

Gnomad4 AFR AF: 0.900

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.808

Gnomad4 EAS AF: 0.698

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.607

Gnomad4 NFE AF: 0.685

Gnomad4 OTH AF: 0.736

Alfa AF: 0.707 Hom.: 38091

Bravo AF: 0.740

Asia WGS AF: 0.585 AC: 2034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.8
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4075052; hg19: chr16-31348233;