rs12403551

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;