rs4620270

Variant names:

• chr8-124425570-G-T
• rs4620270

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.303 in 151,858 control chromosomes in the GnomAD database, including 10,257 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 0.30 (10257 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.280
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.627 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: 0.302 AC: 45898 AN: 151740 Hom.: 10219 Cov.: 31

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.303 AC: 45991 AN: 151858 Hom.: 10257 Cov.: 31 AF XY: 0.304 AC XY: 22573 AN XY: 74216

African (AFR) AF: 0.633 AC: 26201 AN: 41366

American (AMR) AF: 0.256 AC: 3917 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 528 AN: 3470

East Asian (EAS) AF: 0.272 AC: 1402 AN: 5162

South Asian (SAS) AF: 0.243 AC: 1166 AN: 4802

European-Finnish (FIN) AF: 0.193 AC: 2035 AN: 10542

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9773 AN: 67932

Other (OTH) AF: 0.258 AC: 544 AN: 2106

Alfa AF: 0.196 Hom.: 7142

Bravo AF: 0.321

Asia WGS AF: 0.294 AC: 1021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.68
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs4620270; hg19: chr8-125437811;