rs12711445

chr1-114310885-G-C

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 0.776 in 152,188 control chromosomes in the GnomAD database, including 48,145 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 0.78 (48145 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.336

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.776 AC: 117981 AN: 152070 Hom.: 48128 Cov.: 31

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.942

Gnomad AMR AF: 0.834

Gnomad ASJ AF: 0.865

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.924

Gnomad FIN AF: 0.918

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.876

Gnomad OTH AF: 0.789

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

GnomAD4 genome AF: 0.776 AC: 118038 AN: 152188 Hom.: 48145 Cov.: 31 AF XY: 0.783 AC XY: 58249 AN XY: 74422

Gnomad4 AFR AF: 0.496

Gnomad4 AMR AF: 0.835

Gnomad4 ASJ AF: 0.865

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.924

Gnomad4 FIN AF: 0.918

Gnomad4 NFE AF: 0.876

Gnomad4 OTH AF: 0.791

Alfa AF: 0.818 Hom.: 6534

Bravo AF: 0.755

Asia WGS AF: 0.934 AC: 3246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.3
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12711445; hg19: chr1-114853507; COSMIC: COSV59989768;