rs10903122

Positions:

• chr1-24977085-A-G

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 0.563 in 152,052 control chromosomes in the GnomAD database, including 24,519 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 (24519 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.93

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.68 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: 0.563 AC: 85526 AN: 151934 Hom.: 24477 Cov.: 32

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.563 AC: 85611 AN: 152052 Hom.: 24519 Cov.: 32 AF XY: 0.574 AC XY: 42691 AN XY: 74324

Gnomad4 AFR AF: 0.592

Gnomad4 AMR AF: 0.674

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.699

Gnomad4 SAS AF: 0.679

Gnomad4 FIN AF: 0.561

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.582

Alfa AF: 0.519 Hom.: 30700

Bravo AF: 0.574

Asia WGS AF: 0.707 AC: 2459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.9
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10903122; hg19: chr1-25303576;