1-22247449-T-C

Position:

• chr1-22247449-T-C

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 0.592 in 152,114 control chromosomes in the GnomAD database, including 27,255 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 0.59 (27255 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.785 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: 0.592 AC: 90036 AN: 151996 Hom.: 27243 Cov.: 33

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.805

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.592 AC: 90100 AN: 152114 Hom.: 27255 Cov.: 33 AF XY: 0.599 AC XY: 44563 AN XY: 74370

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.629

Gnomad4 ASJ AF: 0.597

Gnomad4 EAS AF: 0.805

Gnomad4 SAS AF: 0.628

Gnomad4 FIN AF: 0.695

Gnomad4 NFE AF: 0.616

Gnomad4 OTH AF: 0.586

Alfa AF: 0.613 Hom.: 24030

Bravo AF: 0.581

Asia WGS AF: 0.732 AC: 2542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.2
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: rs909814; hg19: chr1-22573942;