1-221644339-C-T

Variant names:

• chr1-221644339-C-T
• rs12744344

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 0.368 in 151,994 control chromosomes in the GnomAD database, including 10,382 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 0.37 (10382 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.39 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: 0.368 AC: 55884 AN: 151876 Hom.: 10365 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.368 AC: 55956 AN: 151994 Hom.: 10382 Cov.: 32 AF XY: 0.364 AC XY: 27048 AN XY: 74296

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.326

Gnomad4 NFE AF: 0.373

Gnomad4 OTH AF: 0.395

Alfa AF: 0.280 Hom.: 926

Bravo AF: 0.375

Asia WGS AF: 0.330 AC: 1150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.5
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12744344; hg19: chr1-221817681; COSMIC: COSV60032151;