rs1472606

Variant names:

• chr5-175591132-G-A
• rs1472606

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 0.707 in 151,894 control chromosomes in the GnomAD database, including 38,239 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 0.71 (38239 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.468

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.786 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: 0.707 AC: 107241 AN: 151776 Hom.: 38190 Cov.: 30

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.805

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.709

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

GnomAD4 genome AF: 0.707 AC: 107344 AN: 151894 Hom.: 38239 Cov.: 30 AF XY: 0.709 AC XY: 52671 AN XY: 74238

Gnomad4 AFR AF: 0.753

Gnomad4 AMR AF: 0.777

Gnomad4 ASJ AF: 0.805

Gnomad4 EAS AF: 0.761

Gnomad4 SAS AF: 0.807

Gnomad4 FIN AF: 0.611

Gnomad4 NFE AF: 0.663

Gnomad4 OTH AF: 0.704

Alfa AF: 0.687 Hom.: 46282

Bravo AF: 0.722

Asia WGS AF: 0.772 AC: 2684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1472606; hg19: chr5-175018135; COSMIC: COSV60237270;