rs1907671

chr12-52889414-C-A

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 0.471 in 151,966 control chromosomes in the GnomAD database, including 17,568 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 0.47 (17568 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.885

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71597 AN: 151848 Hom.: 17555 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.471 AC: 71644 AN: 151966 Hom.: 17568 Cov.: 32 AF XY: 0.475 AC XY: 35304 AN XY: 74258

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.613

Gnomad4 SAS AF: 0.704

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.512

Gnomad4 OTH AF: 0.492

Alfa AF: 0.510 Hom.: 32459

Bravo AF: 0.474

Asia WGS AF: 0.580 AC: 2017 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	6.3
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: rs1907671; hg19: chr12-53283198;