1-12211446-T-C

Variant names:

• chr1-12211446-T-C
• rs235214

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 16 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.834 AC: 34612 AN: 41512

American (AMR) AF: 0.800 AC: 12217 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.800 AC: 2776 AN: 3472

East Asian (EAS) AF: 0.549 AC: 2834 AN: 5166

South Asian (SAS) AF: 0.776 AC: 3736 AN: 4816

European-Finnish (FIN) AF: 0.875 AC: 9262 AN: 10588

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.855 AC: 58135 AN: 67998

Other (OTH) AF: 0.841 AC: 1778 AN: 2114

Alfa AF: 0.839 Hom.: 112114

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs235214; hg19: chr1-12271503;