1-22376365-G-T

Variant names:

• chr1-22376365-G-T
• rs6696981

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 45 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.241 AC: 10017 AN: 41502

American (AMR) AF: 0.104 AC: 1598 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0637 AC: 221 AN: 3472

East Asian (EAS) AF: 0.211 AC: 1091 AN: 5166

South Asian (SAS) AF: 0.158 AC: 762 AN: 4818

European-Finnish (FIN) AF: 0.0692 AC: 734 AN: 10606

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7881 AN: 68004

Other (OTH) AF: 0.142 AC: 299 AN: 2108

Alfa AF: 0.125 Hom.: 6337

Bravo AF: 0.157

Asia WGS AF: 0.187 AC: 653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.028
DANN	Benign	0.51
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs6696981; hg19: chr1-22702858;