rs10888557

chr1-153352574-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 0.156 in 152,090 control chromosomes in the GnomAD database, including 2,326 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 0.16 (2326 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490

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 = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23673 AN: 151972 Hom.: 2315 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.0860

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0996

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.156 AC: 23723 AN: 152090 Hom.: 2326 Cov.: 32 AF XY: 0.155 AC XY: 11490 AN XY: 74338

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.0860

Gnomad4 NFE AF: 0.0995

Gnomad4 OTH AF: 0.153

Alfa AF: 0.126 Hom.: 205

Bravo AF: 0.166

Asia WGS AF: 0.182 AC: 636 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	1.3
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10888557; hg19: chr1-153325050;