rs12403551

Variant names:

• chr1-101398659-G-A
• rs12403551

Your query was ambiguous. Multiple possible variants found:

• chr1-101398659-G-A
• chr1-101398659-G-T

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 0.431 in 151,380 control chromosomes in the GnomAD database, including 14,627 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 0.43 (14627 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.763

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.495 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: 0.431 AC: 65251 AN: 151262 Hom.: 14629 Cov.: 31

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.431 AC: 65267 AN: 151380 Hom.: 14627 Cov.: 31 AF XY: 0.433 AC XY: 32010 AN XY: 73886

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.502

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.434

Alfa AF: 0.466 Hom.: 34139

Bravo AF: 0.419

Asia WGS AF: 0.441 AC: 1534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.23
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12403551; hg19: chr1-101864215;