rs10925567

Variant names:

• chr1-238121211-T-A
• rs10925567

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 0.0526 in 152,272 control chromosomes in the GnomAD database, including 260 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 0.053 (260 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.449

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.089 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: 0.0525 AC: 7992 AN: 152154 Hom.: 259 Cov.: 32

Gnomad AFR AF: 0.0912

Gnomad AMI AF: 0.0176

Gnomad AMR AF: 0.0259

Gnomad ASJ AF: 0.0331

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0499

Gnomad FIN AF: 0.0209

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0460

Gnomad OTH AF: 0.0406

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

GnomAD4 genome AF: 0.0526 AC: 8008 AN: 152272 Hom.: 260 Cov.: 32 AF XY: 0.0506 AC XY: 3772 AN XY: 74478

Gnomad4 AFR AF: 0.0914

Gnomad4 AMR AF: 0.0259

Gnomad4 ASJ AF: 0.0331

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0499

Gnomad4 FIN AF: 0.0209

Gnomad4 NFE AF: 0.0460

Gnomad4 OTH AF: 0.0402

Alfa AF: 0.0521 Hom.: 25

Bravo AF: 0.0528

Asia WGS AF: 0.0370 AC: 127 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.085
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10925567; hg19: chr1-238284511;