chr1-22376365-G-T

Position:

• chr1-22376365-G-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 0.15 in 152,174 control chromosomes in the GnomAD database, including 2,040 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 0.15 (2040 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.22376365G>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22744 AN: 152056 Hom.: 2036 Cov.: 33

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0637

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.0692

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.150 AC: 22767 AN: 152174 Hom.: 2040 Cov.: 33 AF XY: 0.146 AC XY: 10875 AN XY: 74406

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.0637

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.0692

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.142

Alfa AF: 0.119 Hom.: 2675

Bravo AF: 0.157

Asia WGS AF: 0.187 AC: 653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.028
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6696981; hg19: chr1-22702858;