5-90122201-A-T

Variant names:

• chr5-90122201-A-T
• rs2973361

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.493 in 152,046 control chromosomes in the GnomAD database, including 18,904 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 0.49 (18904 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.591 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: 0.493 AC: 74839 AN: 151930 Hom.: 18884 Cov.: 32

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.493 AC: 74891 AN: 152046 Hom.: 18904 Cov.: 32 AF XY: 0.494 AC XY: 36748 AN XY: 74332

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.601

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.587

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.505

Alfa AF: 0.494 Hom.: 2349

Bravo AF: 0.496

Asia WGS AF: 0.567 AC: 1970 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2973361; hg19: chr5-89418018;