rs10900594

chr1-204501001-G-Cchr1-204501001-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 0.587 in 152,012 control chromosomes in the GnomAD database, including 28,444 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 0.59 (28444 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.993

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.587 AC: 89215 AN: 151892 Hom.: 28440 Cov.: 31

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.587 AC: 89235 AN: 152012 Hom.: 28444 Cov.: 31 AF XY: 0.594 AC XY: 44100 AN XY: 74290

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.609

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.680

Gnomad4 SAS AF: 0.608

Gnomad4 FIN AF: 0.811

Gnomad4 NFE AF: 0.697

Gnomad4 OTH AF: 0.589

Alfa AF: 0.561 Hom.: 2002

Bravo AF: 0.561

Asia WGS AF: 0.596 AC: 2074 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	0.30
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10900594; hg19: chr1-204470129;