1-23869911-A-G

Variant names:

• chr1-23869911-A-G
• rs3123554

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 0.634 in 151,468 control chromosomes in the GnomAD database, including 30,851 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 0.63 (30851 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178
• Publications: 28 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.749 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: 0.634 AC: 95974 AN: 151350 Hom.: 30841 Cov.: 28

Gnomad AFR AF: 0.757

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.634 AC: 96026 AN: 151468 Hom.: 30851 Cov.: 28 AF XY: 0.637 AC XY: 47119 AN XY: 73960

African (AFR) AF: 0.756 AC: 31221 AN: 41298

American (AMR) AF: 0.640 AC: 9740 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2012 AN: 3466

East Asian (EAS) AF: 0.524 AC: 2675 AN: 5102

South Asian (SAS) AF: 0.713 AC: 3415 AN: 4790

European-Finnish (FIN) AF: 0.575 AC: 6012 AN: 10450

Middle Eastern (MID) AF: 0.690 AC: 200 AN: 290

European-Non Finnish (NFE) AF: 0.574 AC: 38961 AN: 67848

Other (OTH) AF: 0.613 AC: 1291 AN: 2106

Alfa AF: 0.600 Hom.: 36330

Bravo AF: 0.644

Asia WGS AF: 0.630 AC: 2191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	14
DANN	Benign	0.81
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs3123554; hg19: chr1-24196401;