rs1145603

chr5-157861421-G-A

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 0.597 in 152,082 control chromosomes in the GnomAD database, including 27,577 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 0.60 (27577 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.684 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: 0.597 AC: 90665 AN: 151964 Hom.: 27533 Cov.: 32

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.597 AC: 90761 AN: 152082 Hom.: 27577 Cov.: 32 AF XY: 0.599 AC XY: 44511 AN XY: 74336

Gnomad4 AFR AF: 0.690

Gnomad4 AMR AF: 0.464

Gnomad4 ASJ AF: 0.619

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.600

Gnomad4 FIN AF: 0.676

Gnomad4 NFE AF: 0.573

Gnomad4 OTH AF: 0.586

Alfa AF: 0.600 Hom.: 3979

Bravo AF: 0.578

Asia WGS AF: 0.505 AC: 1757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	11
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1145603; hg19: chr5-157288429;