rs10881542

Variant names:

• chr1-104310116-T-C
• rs10881542

Your query was ambiguous. Multiple possible variants found:

• chr1-104310116-T-C
• chr1-104310116-T-G

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 0.517 in 152,068 control chromosomes in the GnomAD database, including 20,627 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 0.52 (20627 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.597 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: 0.517 AC: 78522 AN: 151950 Hom.: 20611 Cov.: 32

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.517 AC: 78584 AN: 152068 Hom.: 20627 Cov.: 32 AF XY: 0.519 AC XY: 38559 AN XY: 74342

African (AFR) AF: 0.575 AC: 23853 AN: 41492

American (AMR) AF: 0.527 AC: 8058 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 1001 AN: 3470

East Asian (EAS) AF: 0.615 AC: 3176 AN: 5162

South Asian (SAS) AF: 0.466 AC: 2241 AN: 4814

European-Finnish (FIN) AF: 0.552 AC: 5845 AN: 10580

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.482 AC: 32757 AN: 67962

Other (OTH) AF: 0.488 AC: 1028 AN: 2108

Alfa AF: 0.502 Hom.: 16483

Bravo AF: 0.519

Asia WGS AF: 0.578 AC: 2005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.78
PhyloP100		-0.039

Splicing

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

Other links and lift over

dbSNP: rs10881542; hg19: chr1-104852738;