rs58845495

Positions:

• chr7-128822793-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;