8-58487781-C-T

Variant names:

• chr8-58487781-C-T
• rs10957057

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 0.116 in 152,106 control chromosomes in the GnomAD database, including 1,137 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 0.12 (1137 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17622 AN: 151986 Hom.: 1138 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.0827

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0642

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.116 AC: 17630 AN: 152106 Hom.: 1137 Cov.: 32 AF XY: 0.111 AC XY: 8283 AN XY: 74368

African (AFR) AF: 0.120 AC: 4977 AN: 41484

American (AMR) AF: 0.0825 AC: 1261 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 641 AN: 3472

East Asian (EAS) AF: 0.172 AC: 889 AN: 5156

South Asian (SAS) AF: 0.101 AC: 489 AN: 4820

European-Finnish (FIN) AF: 0.0642 AC: 680 AN: 10584

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8281 AN: 67994

Other (OTH) AF: 0.126 AC: 266 AN: 2112

Alfa AF: 0.120 Hom.: 2036

Bravo AF: 0.118

Asia WGS AF: 0.140 AC: 488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.088
DANN	Benign	0.94
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs10957057; hg19: chr8-59400340;