rs1562435

chr8-127494212-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.32 in 152,150 control chromosomes in the GnomAD database, including 8,056 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 0.32 (8056 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.74

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.359 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: 0.320 AC: 48711 AN: 152032 Hom.: 8054 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.320 AC: 48721 AN: 152150 Hom.: 8056 Cov.: 32 AF XY: 0.316 AC XY: 23501 AN XY: 74384

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.328

Gnomad4 EAS AF: 0.117

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.316

Alfa AF: 0.330 Hom.: 1475

Bravo AF: 0.318

Asia WGS AF: 0.211 AC: 738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
Cadd	Benign	18
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1562435; hg19: chr8-128506457;