rs1562435

Variant names:

• chr8-127494212-A-G
• rs1562435

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.299 AC: 12402 AN: 41508

American (AMR) AF: 0.303 AC: 4640 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1138 AN: 3466

East Asian (EAS) AF: 0.117 AC: 605 AN: 5188

South Asian (SAS) AF: 0.314 AC: 1513 AN: 4820

European-Finnish (FIN) AF: 0.260 AC: 2745 AN: 10558

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24682 AN: 68006

Other (OTH) AF: 0.316 AC: 667 AN: 2108

Alfa AF: 0.329 Hom.: 1738

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
PhyloP100		2.7

Splicing

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

Other links and lift over

dbSNP: rs1562435; hg19: chr8-128506457;