rs7442675

Variant names:

• chr5-52273708-G-A
• rs7442675

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 0.0672 in 152,016 control chromosomes in the GnomAD database, including 406 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 0.067 (406 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.519
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.112 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: 0.0671 AC: 10196 AN: 151898 Hom.: 404 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0404

Gnomad ASJ AF: 0.0482

Gnomad EAS AF: 0.000581

Gnomad SAS AF: 0.0790

Gnomad FIN AF: 0.0494

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0530

Gnomad OTH AF: 0.0703

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

GnomAD4 genome AF: 0.0672 AC: 10215 AN: 152016 Hom.: 406 Cov.: 32 AF XY: 0.0668 AC XY: 4961 AN XY: 74294

African (AFR) AF: 0.114 AC: 4746 AN: 41478

American (AMR) AF: 0.0403 AC: 614 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.0482 AC: 167 AN: 3466

East Asian (EAS) AF: 0.000582 AC: 3 AN: 5154

South Asian (SAS) AF: 0.0803 AC: 387 AN: 4818

European-Finnish (FIN) AF: 0.0494 AC: 522 AN: 10572

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0530 AC: 3605 AN: 67976

Other (OTH) AF: 0.0691 AC: 146 AN: 2112

Alfa AF: 0.0580 Hom.: 142

Bravo AF: 0.0672

Asia WGS AF: 0.0340 AC: 119 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.87
DANN	Benign	0.68
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs7442675; hg19: chr5-51569542;