rs7550692

Variant names:

• chr1-162059501-C-T
• rs7550692

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 0.402 in 150,708 control chromosomes in the GnomAD database, including 12,872 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 0.40 (12872 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.823
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.63 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: 0.402 AC: 60596 AN: 150588 Hom.: 12873 Cov.: 29

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.402 AC: 60619 AN: 150708 Hom.: 12872 Cov.: 29 AF XY: 0.407 AC XY: 29943 AN XY: 73556

African (AFR) AF: 0.502 AC: 20473 AN: 40814

American (AMR) AF: 0.379 AC: 5740 AN: 15144

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1333 AN: 3464

East Asian (EAS) AF: 0.531 AC: 2712 AN: 5112

South Asian (SAS) AF: 0.649 AC: 3105 AN: 4784

European-Finnish (FIN) AF: 0.353 AC: 3660 AN: 10356

Middle Eastern (MID) AF: 0.390 AC: 114 AN: 292

European-Non Finnish (NFE) AF: 0.329 AC: 22312 AN: 67746

Other (OTH) AF: 0.397 AC: 830 AN: 2090

Alfa AF: 0.362 Hom.: 15205

Bravo AF: 0.402

Asia WGS AF: 0.589 AC: 2047 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	7.5
DANN	Benign	0.55
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs7550692; hg19: chr1-162029291;