5-83602427-T-G

Variant names:

• chr5-83602427-T-G
• rs309570

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 0.323 in 152,102 control chromosomes in the GnomAD database, including 8,433 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 (8433 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.462 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: 0.323 AC: 49060 AN: 151982 Hom.: 8419 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.323 AC: 49093 AN: 152102 Hom.: 8433 Cov.: 32 AF XY: 0.325 AC XY: 24126 AN XY: 74332

African (AFR) AF: 0.220 AC: 9141 AN: 41510

American (AMR) AF: 0.471 AC: 7190 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1144 AN: 3468

East Asian (EAS) AF: 0.404 AC: 2081 AN: 5154

South Asian (SAS) AF: 0.395 AC: 1902 AN: 4814

European-Finnish (FIN) AF: 0.317 AC: 3355 AN: 10588

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.338 AC: 22977 AN: 67976

Other (OTH) AF: 0.354 AC: 749 AN: 2116

Alfa AF: 0.332 Hom.: 22585

Bravo AF: 0.329

Asia WGS AF: 0.393 AC: 1363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.55
DANN	Benign	0.44
PhyloP100		-0.047

Splicing

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

Other links and lift over

dbSNP: rs309570; hg19: chr5-82898246; COSMIC: COSV60160883;