rs1356752

Positions:

• chr8-49438311-A-G
• chr8-49438311-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 0.803 in 151,922 control chromosomes in the GnomAD database, including 53,091 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 0.80 (53091 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.803 AC: 121944 AN: 151804 Hom.: 53083 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.988

Gnomad AMR AF: 0.903

Gnomad ASJ AF: 0.938

Gnomad EAS AF: 0.973

Gnomad SAS AF: 0.952

Gnomad FIN AF: 0.959

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.950

Gnomad OTH AF: 0.839

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

GnomAD4 genome AF: 0.803 AC: 121984 AN: 151922 Hom.: 53091 Cov.: 32 AF XY: 0.808 AC XY: 60050 AN XY: 74294

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.903

Gnomad4 ASJ AF: 0.938

Gnomad4 EAS AF: 0.973

Gnomad4 SAS AF: 0.952

Gnomad4 FIN AF: 0.959

Gnomad4 NFE AF: 0.950

Gnomad4 OTH AF: 0.840

Alfa AF: 0.654 Hom.: 5747

Bravo AF: 0.783

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.38
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1356752; hg19: chr8-50350870;