chr1-23869911-A-G

Variant names:

• chr1-23869911-A-G
• rs3123554

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 0.634 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.756

Gnomad4 AMR AF: 0.640

Gnomad4 ASJ AF: 0.580

Gnomad4 EAS AF: 0.524

Gnomad4 SAS AF: 0.713

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.574

Gnomad4 OTH AF: 0.613

Alfa AF: 0.592 Hom.: 27028

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3123554; hg19: chr1-24196401;