rs10900594

Variant names:

• chr1-204501001-G-C
• rs10900594

Your query was ambiguous. Multiple possible variants found:

• chr1-204501001-G-C
• chr1-204501001-G-T

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 0.587 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
• Publications: 15 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 (NFE) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.320 AC: 13252 AN: 41424

American (AMR) AF: 0.609 AC: 9293 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2129 AN: 3466

East Asian (EAS) AF: 0.680 AC: 3517 AN: 5170

South Asian (SAS) AF: 0.608 AC: 2934 AN: 4822

European-Finnish (FIN) AF: 0.811 AC: 8589 AN: 10586

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.697 AC: 47389 AN: 67968

Other (OTH) AF: 0.589 AC: 1242 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.30
DANN	Benign	0.70
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs10900594; hg19: chr1-204470129;