rs180557

Variant names:

• chr10-116055375-G-A
• rs180557

Your query was ambiguous. Multiple possible variants found:

• chr10-116055375-G-A
• chr10-116055375-G-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 0.232 in 152,086 control chromosomes in the GnomAD database, including 4,903 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 0.23 (4903 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 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: 0.232 AC: 35298 AN: 151968 Hom.: 4894 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.232 AC: 35342 AN: 152086 Hom.: 4903 Cov.: 32 AF XY: 0.230 AC XY: 17118 AN XY: 74348

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.228

Alfa AF: 0.151 Hom.: 385

Bravo AF: 0.235

Asia WGS AF: 0.192 AC: 667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.18
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs180557; hg19: chr10-117814886;