rs1419772

Variant names:

• chr7-22058608-C-T
• rs1419772

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 0.274 in 152,030 control chromosomes in the GnomAD database, including 6,837 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 0.27 (6837 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.366 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: 0.274 AC: 41655 AN: 151912 Hom.: 6831 Cov.: 33

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.0185

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.274 AC: 41683 AN: 152030 Hom.: 6837 Cov.: 33 AF XY: 0.271 AC XY: 20098 AN XY: 74298

African (AFR) AF: 0.115 AC: 4771 AN: 41488

American (AMR) AF: 0.286 AC: 4366 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1533 AN: 3470

East Asian (EAS) AF: 0.0184 AC: 95 AN: 5170

South Asian (SAS) AF: 0.264 AC: 1272 AN: 4812

European-Finnish (FIN) AF: 0.331 AC: 3481 AN: 10532

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.370 AC: 25132 AN: 67960

Other (OTH) AF: 0.283 AC: 598 AN: 2112

Alfa AF: 0.308 Hom.: 1300

Bravo AF: 0.264

Asia WGS AF: 0.154 AC: 538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	11
DANN	Benign	0.49
PhyloP100		-0.044

Splicing

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

Other links and lift over

dbSNP: rs1419772; hg19: chr7-22098226;