chr1-227501932-T-C

Variant names:

• chr1-227501932-T-C
• rs2814064

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 0.431 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.594 AC: 24598 AN: 41434

American (AMR) AF: 0.405 AC: 6195 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 969 AN: 3472

East Asian (EAS) AF: 0.506 AC: 2615 AN: 5168

South Asian (SAS) AF: 0.399 AC: 1919 AN: 4806

European-Finnish (FIN) AF: 0.419 AC: 4417 AN: 10530

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.346 AC: 23478 AN: 67934

Other (OTH) AF: 0.396 AC: 837 AN: 2112

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

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