7-22745364-T-G

Variant names:

• chr7-22745364-T-G
• rs1524106

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 0.434 in 151,998 control chromosomes in the GnomAD database, including 16,364 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 0.43 (16364 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.917 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65789 AN: 151882 Hom.: 16325 Cov.: 31

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.939

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.434 AC: 65895 AN: 151998 Hom.: 16364 Cov.: 31 AF XY: 0.440 AC XY: 32717 AN XY: 74326

African (AFR) AF: 0.550 AC: 22779 AN: 41430

American (AMR) AF: 0.565 AC: 8621 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1803 AN: 3472

East Asian (EAS) AF: 0.940 AC: 4861 AN: 5174

South Asian (SAS) AF: 0.636 AC: 3070 AN: 4828

European-Finnish (FIN) AF: 0.228 AC: 2416 AN: 10578

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.306 AC: 20769 AN: 67946

Other (OTH) AF: 0.488 AC: 1028 AN: 2106

Alfa AF: 0.354 Hom.: 2259

Bravo AF: 0.465

Asia WGS AF: 0.778 AC: 2698 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.3
DANN	Benign	0.72
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs1524106; hg19: chr7-22784983;