rs10888557

Variant names:

• chr1-153352574-G-C
• rs10888557

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 0.156 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.271 AC: 11242 AN: 41462

American (AMR) AF: 0.140 AC: 2140 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 503 AN: 3472

East Asian (EAS) AF: 0.187 AC: 965 AN: 5160

South Asian (SAS) AF: 0.157 AC: 755 AN: 4818

European-Finnish (FIN) AF: 0.0860 AC: 910 AN: 10580

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0995 AC: 6768 AN: 67992

Other (OTH) AF: 0.153 AC: 322 AN: 2104

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
PhyloP100		-0.049

Splicing

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

Other links and lift over

dbSNP: rs10888557; hg19: chr1-153325050;