rs1472606

Variant names:

• chr5-175591132-G-A
• rs1472606

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.753 AC: 31196 AN: 41426

American (AMR) AF: 0.777 AC: 11848 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.805 AC: 2790 AN: 3464

East Asian (EAS) AF: 0.761 AC: 3908 AN: 5134

South Asian (SAS) AF: 0.807 AC: 3898 AN: 4828

European-Finnish (FIN) AF: 0.611 AC: 6444 AN: 10544

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.663 AC: 45027 AN: 67934

Other (OTH) AF: 0.704 AC: 1485 AN: 2108

Alfa AF: 0.690 Hom.: 59686

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
PhyloP100		-0.47

Splicing

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

Other links and lift over

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