1-205137154-A-G

Variant names:

• chr1-205137154-A-G
• rs10900451

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 0.803 in 151,732 control chromosomes in the GnomAD database, including 50,453 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 0.80 (50453 hom., cov: 31)
• Consequence: LOC124904585 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 7 publications found

Genes affected

LOC124904585 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000825123.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307332	ENST00000825123.1		n.305-3004A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.803 AC: 121744 AN: 151614 Hom.: 50439 Cov.: 31

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.929

Gnomad AMR AF: 0.882

Gnomad ASJ AF: 0.871

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.913

Gnomad FIN AF: 0.916

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.870

Gnomad OTH AF: 0.842

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

GnomAD4 genome AF: 0.803 AC: 121794 AN: 151732 Hom.: 50453 Cov.: 31 AF XY: 0.808 AC XY: 59920 AN XY: 74198

African (AFR) AF: 0.587 AC: 24110 AN: 41042

American (AMR) AF: 0.882 AC: 13480 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.871 AC: 3021 AN: 3470

East Asian (EAS) AF: 0.970 AC: 5024 AN: 5180

South Asian (SAS) AF: 0.913 AC: 4399 AN: 4818

European-Finnish (FIN) AF: 0.916 AC: 9717 AN: 10608

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.870 AC: 59158 AN: 68014

Other (OTH) AF: 0.844 AC: 1781 AN: 2110

Alfa AF: 0.837 Hom.: 9159

Bravo AF: 0.793

Asia WGS AF: 0.931 AC: 3234 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.69
DANN	Benign	0.30
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10900451; hg19: chr1-205106282;