1-227501932-T-C

Variant names:

• chr1-227501932-T-C
• rs2814064

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 0.431 in 151,948 control chromosomes in the GnomAD database, including 15,020 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 0.43 (15020 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.587 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: 0.431 AC: 65398 AN: 151830 Hom.: 14988 Cov.: 31

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.431 AC: 65483 AN: 151948 Hom.: 15020 Cov.: 31 AF XY: 0.433 AC XY: 32174 AN XY: 74268

Gnomad4 AFR AF: 0.594

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.506

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.419

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.396

Alfa AF: 0.405 Hom.: 2006

Bravo AF: 0.443

Asia WGS AF: 0.413 AC: 1441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.63
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2814064; hg19: chr1-227689633; COSMIC: COSV69712367;