1-212427175-C-T

Variant names:

• chr1-212427175-C-T
• rs640526

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 0.784 in 151,568 control chromosomes in the GnomAD database, including 47,571 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 (47571 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.972

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.933 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: 0.784 AC: 118693 AN: 151448 Hom.: 47528 Cov.: 27

Gnomad AFR AF: 0.941

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.759

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

GnomAD4 genome AF: 0.784 AC: 118791 AN: 151568 Hom.: 47571 Cov.: 27 AF XY: 0.774 AC XY: 57321 AN XY: 74042

Gnomad4 AFR AF: 0.941

Gnomad4 AMR AF: 0.752

Gnomad4 ASJ AF: 0.725

Gnomad4 EAS AF: 0.611

Gnomad4 SAS AF: 0.524

Gnomad4 FIN AF: 0.685

Gnomad4 NFE AF: 0.746

Gnomad4 OTH AF: 0.756

Alfa AF: 0.757 Hom.: 5476

Bravo AF: 0.802

Asia WGS AF: 0.555 AC: 1929 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs640526; hg19: chr1-212600517;