1-22349799-T-C

Position:

• chr1-22349799-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 0.647 in 152,054 control chromosomes in the GnomAD database, including 31,948 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 0.65 (31948 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.646 AC: 98225 AN: 151936 Hom.: 31901 Cov.: 33

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.647 AC: 98328 AN: 152054 Hom.: 31948 Cov.: 33 AF XY: 0.647 AC XY: 48110 AN XY: 74330

Gnomad4 AFR AF: 0.711

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.740

Gnomad4 SAS AF: 0.671

Gnomad4 FIN AF: 0.628

Gnomad4 NFE AF: 0.616

Gnomad4 OTH AF: 0.605

Alfa AF: 0.636 Hom.: 3823

Bravo AF: 0.647

Asia WGS AF: 0.722 AC: 2511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.8
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4233285; hg19: chr1-22676292;