1-221644339-C-T

Variant names:

• chr1-221644339-C-T
• rs12744344

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 0.368 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.396 AC: 16400 AN: 41462

American (AMR) AF: 0.356 AC: 5433 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1229 AN: 3466

East Asian (EAS) AF: 0.282 AC: 1455 AN: 5166

South Asian (SAS) AF: 0.293 AC: 1410 AN: 4812

European-Finnish (FIN) AF: 0.326 AC: 3445 AN: 10570

Middle Eastern (MID) AF: 0.497 AC: 145 AN: 292

European-Non Finnish (NFE) AF: 0.373 AC: 25369 AN: 67938

Other (OTH) AF: 0.395 AC: 836 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.5
DANN	Benign	0.63
PhyloP100		-0.064

Splicing

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

Other links and lift over

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