rs4552913

Variant names:

• chr8-143564835-G-A
• rs4552913

Your query was ambiguous. Multiple possible variants found:

• chr8-143564835-G-A
• chr8-143564835-G-C
• chr8-143564835-G-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 0.757 in 152,220 control chromosomes in the GnomAD database, including 44,150 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 0.76 (44150 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.43

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.949 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: 0.757 AC: 115148 AN: 152102 Hom.: 44145 Cov.: 34

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.835

Gnomad EAS AF: 0.971

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.852

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.757 AC: 115190 AN: 152220 Hom.: 44150 Cov.: 34 AF XY: 0.766 AC XY: 57024 AN XY: 74434

Gnomad4 AFR AF: 0.625

Gnomad4 AMR AF: 0.808

Gnomad4 ASJ AF: 0.835

Gnomad4 EAS AF: 0.971

Gnomad4 SAS AF: 0.833

Gnomad4 FIN AF: 0.852

Gnomad4 NFE AF: 0.785

Gnomad4 OTH AF: 0.746

Alfa AF: 0.774 Hom.: 9460

Bravo AF: 0.749

Asia WGS AF: 0.857 AC: 2979 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.29
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4552913; hg19: chr8-144647005;