1-22247449-T-C

Variant names:

• chr1-22247449-T-C
• rs909814

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;