1-203396104-A-G

Variant names:

• chr1-203396104-A-G
• rs10800925
• XR_001738385.2:n.701A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_922438.3(LOC102723529):​n.905A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 151,794 control chromosomes in the GnomAD database, including 17,011 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 0.46 (17011 hom., cov: 31)
• Consequence: LOC102723529 XR_922438.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.788
• Publications: 9 publications found

Genes affected

LOC102723529 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000771306.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300395	ENST00000771306.1		n.680-911A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69113 AN: 151676 Hom.: 17010 Cov.: 31

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.755

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.455 AC: 69132 AN: 151794 Hom.: 17011 Cov.: 31 AF XY: 0.454 AC XY: 33666 AN XY: 74186

African (AFR) AF: 0.270 AC: 11194 AN: 41388

American (AMR) AF: 0.509 AC: 7762 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1680 AN: 3466

East Asian (EAS) AF: 0.312 AC: 1603 AN: 5146

South Asian (SAS) AF: 0.431 AC: 2077 AN: 4814

European-Finnish (FIN) AF: 0.541 AC: 5679 AN: 10504

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37277 AN: 67906

Other (OTH) AF: 0.488 AC: 1025 AN: 2102

Alfa AF: 0.519 Hom.: 89326

Bravo AF: 0.445

Asia WGS AF: 0.398 AC: 1386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.1
DANN	Benign	0.76
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs10800925; hg19: chr1-203365232;