rs58845495

Variant names:

• chr7-128822793-T-C
• rs58845495

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 0.094 in 152,126 control chromosomes in the GnomAD database, including 690 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 0.094 (690 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350

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 (EAS) allele frequency at 95% confidence interval = 0.181 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: 0.0940 AC: 14282 AN: 152008 Hom.: 688 Cov.: 32

Gnomad AFR AF: 0.0980

Gnomad AMI AF: 0.0736

Gnomad AMR AF: 0.0885

Gnomad ASJ AF: 0.0988

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.0847

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0863

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.0940 AC: 14302 AN: 152126 Hom.: 690 Cov.: 32 AF XY: 0.0941 AC XY: 6996 AN XY: 74362

Gnomad4 AFR AF: 0.0981

Gnomad4 AMR AF: 0.0884

Gnomad4 ASJ AF: 0.0988

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.0999

Gnomad4 FIN AF: 0.0847

Gnomad4 NFE AF: 0.0863

Gnomad4 OTH AF: 0.107

Alfa AF: 0.0929 Hom.: 82

Bravo AF: 0.0953

Asia WGS AF: 0.148 AC: 513 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	4.5
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs58845495; hg19: chr7-128462847;