rs10920212

Positions:

• chr1-201477345-G-T

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 0.557 in 152,028 control chromosomes in the GnomAD database, including 24,821 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 0.56 (24821 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.221

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84622 AN: 151910 Hom.: 24815 Cov.: 32

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.557 AC: 84643 AN: 152028 Hom.: 24821 Cov.: 32 AF XY: 0.548 AC XY: 40725 AN XY: 74300

Gnomad4 AFR AF: 0.454

Gnomad4 AMR AF: 0.515

Gnomad4 ASJ AF: 0.669

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.572

Gnomad4 NFE AF: 0.660

Gnomad4 OTH AF: 0.558

Alfa AF: 0.629 Hom.: 22768

Bravo AF: 0.548

Asia WGS AF: 0.299 AC: 1044 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.77
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10920212; hg19: chr1-201446473;