rs1145603

Variant names:

• chr5-157861421-G-A
• rs1145603

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;