rs1990745

Variant names:

• chr5-104046221-T-C
• rs1990745

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 0.838 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
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.943 AC: 39176 AN: 41550

American (AMR) AF: 0.688 AC: 10516 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.762 AC: 2645 AN: 3470

East Asian (EAS) AF: 0.391 AC: 2024 AN: 5170

South Asian (SAS) AF: 0.687 AC: 3320 AN: 4830

European-Finnish (FIN) AF: 0.765 AC: 8102 AN: 10594

Middle Eastern (MID) AF: 0.839 AC: 245 AN: 292

European-Non Finnish (NFE) AF: 0.867 AC: 58998 AN: 68012

Other (OTH) AF: 0.816 AC: 1725 AN: 2114

Alfa AF: 0.846 Hom.: 92724

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
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs1990745; hg19: chr5-103381922;