rs607145

Variant names:

• chr5-41579023-G-A
• rs607145

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 0.103 in 152,220 control chromosomes in the GnomAD database, including 965 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 0.10 (965 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.601

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.174 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: 0.103 AC: 15662 AN: 152102 Hom.: 963 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0844

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.00405

Gnomad SAS AF: 0.0638

Gnomad FIN AF: 0.0471

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0802

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.103 AC: 15665 AN: 152220 Hom.: 965 Cov.: 32 AF XY: 0.100 AC XY: 7452 AN XY: 74416

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.0842

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.00406

Gnomad4 SAS AF: 0.0630

Gnomad4 FIN AF: 0.0471

Gnomad4 NFE AF: 0.0802

Gnomad4 OTH AF: 0.108

Alfa AF: 0.0899 Hom.: 362

Bravo AF: 0.110

Asia WGS AF: 0.0500 AC: 174 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.4
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs607145; hg19: chr5-41579125;