5-42395179-A-T

Variant names:

• chr5-42395179-A-T
• rs1858138

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 0.509 in 151,992 control chromosomes in the GnomAD database, including 20,885 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 0.51 (20885 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.138
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.866 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: 0.509 AC: 77283 AN: 151874 Hom.: 20871 Cov.: 33

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.388

Gnomad NFE AF: 0.554

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.509 AC: 77342 AN: 151992 Hom.: 20885 Cov.: 33 AF XY: 0.515 AC XY: 38251 AN XY: 74304

African (AFR) AF: 0.345 AC: 14331 AN: 41484

American (AMR) AF: 0.529 AC: 8080 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1852 AN: 3472

East Asian (EAS) AF: 0.888 AC: 4587 AN: 5168

South Asian (SAS) AF: 0.657 AC: 3170 AN: 4826

European-Finnish (FIN) AF: 0.585 AC: 6170 AN: 10554

Middle Eastern (MID) AF: 0.410 AC: 119 AN: 290

European-Non Finnish (NFE) AF: 0.554 AC: 37619 AN: 67896

Other (OTH) AF: 0.500 AC: 1055 AN: 2112

Alfa AF: 0.512 Hom.: 2553

Bravo AF: 0.497

Asia WGS AF: 0.747 AC: 2594 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.65
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs1858138; hg19: chr5-42395281;