rs1592749

Positions:

• chr5-160545014-T-G

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 0.705 in 151,910 control chromosomes in the GnomAD database, including 38,361 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 0.70 (38361 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 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: 0.705 AC: 106971 AN: 151792 Hom.: 38299 Cov.: 31

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.990

Gnomad SAS AF: 0.793

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.705 AC: 107096 AN: 151910 Hom.: 38361 Cov.: 31 AF XY: 0.710 AC XY: 52680 AN XY: 74224

Gnomad4 AFR AF: 0.792

Gnomad4 AMR AF: 0.758

Gnomad4 ASJ AF: 0.687

Gnomad4 EAS AF: 0.990

Gnomad4 SAS AF: 0.793

Gnomad4 FIN AF: 0.612

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.697

Alfa AF: 0.666 Hom.: 17479

Bravo AF: 0.721

Asia WGS AF: 0.898 AC: 3121 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.6
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1592749; hg19: chr5-159972021;