rs235214

Positions:

• chr1-12211446-T-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 0.83 in 152,150 control chromosomes in the GnomAD database, including 52,680 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 0.83 (52680 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.849 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: 0.830 AC: 126202 AN: 152032 Hom.: 52631 Cov.: 31

Gnomad AFR AF: 0.833

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.875

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.855

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.830 AC: 126302 AN: 152150 Hom.: 52680 Cov.: 31 AF XY: 0.830 AC XY: 61699 AN XY: 74370

Gnomad4 AFR AF: 0.834

Gnomad4 AMR AF: 0.800

Gnomad4 ASJ AF: 0.800

Gnomad4 EAS AF: 0.549

Gnomad4 SAS AF: 0.776

Gnomad4 FIN AF: 0.875

Gnomad4 NFE AF: 0.855

Gnomad4 OTH AF: 0.841

Alfa AF: 0.843 Hom.: 30002

Bravo AF: 0.827

Asia WGS AF: 0.650 AC: 2259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs235214; hg19: chr1-12271503;