1-221541794-C-T

Position:

• chr1-221541794-C-T

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 0.0515 in 152,224 control chromosomes in the GnomAD database, including 311 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 0.052 (311 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0514 AC: 7824 AN: 152106 Hom.: 309 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0343

Gnomad ASJ AF: 0.0279

Gnomad EAS AF: 0.0549

Gnomad SAS AF: 0.0549

Gnomad FIN AF: 0.0155

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0251

Gnomad OTH AF: 0.0402

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

GnomAD4 genome AF: 0.0515 AC: 7844 AN: 152224 Hom.: 311 Cov.: 32 AF XY: 0.0497 AC XY: 3698 AN XY: 74410

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.0342

Gnomad4 ASJ AF: 0.0279

Gnomad4 EAS AF: 0.0548

Gnomad4 SAS AF: 0.0548

Gnomad4 FIN AF: 0.0155

Gnomad4 NFE AF: 0.0251

Gnomad4 OTH AF: 0.0407

Alfa AF: 0.0309 Hom.: 91

Bravo AF: 0.0545

Asia WGS AF: 0.0590 AC: 205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.081
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11118748; hg19: chr1-221715136;