rs1990745

Positions:

• chr5-104046221-T-C

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 0.838 in 152,230 control chromosomes in the GnomAD database, including 54,644 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 0.84 (54644 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.842

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.935 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.838 AC: 127453 AN: 152112 Hom.: 54593 Cov.: 33

Gnomad AFR AF: 0.943

Gnomad AMI AF: 0.882

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.834

Gnomad NFE AF: 0.867

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.838 AC: 127555 AN: 152230 Hom.: 54644 Cov.: 33 AF XY: 0.825 AC XY: 61368 AN XY: 74406

Gnomad4 AFR AF: 0.943

Gnomad4 AMR AF: 0.688

Gnomad4 ASJ AF: 0.762

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.687

Gnomad4 FIN AF: 0.765

Gnomad4 NFE AF: 0.867

Gnomad4 OTH AF: 0.816

Alfa AF: 0.846 Hom.: 69971

Bravo AF: 0.836

Asia WGS AF: 0.512 AC: 1784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	13
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1990745; hg19: chr5-103381922;