chr7-35522260-T-C

Variant names:

• chr7-35522260-T-C
• rs867177

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 0.261 in 152,028 control chromosomes in the GnomAD database, including 5,946 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 0.26 (5946 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0660
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.469 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: 0.260 AC: 39571 AN: 151910 Hom.: 5935 Cov.: 33

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.261 AC: 39608 AN: 152028 Hom.: 5946 Cov.: 33 AF XY: 0.266 AC XY: 19755 AN XY: 74318

African (AFR) AF: 0.126 AC: 5227 AN: 41488

American (AMR) AF: 0.320 AC: 4891 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 882 AN: 3470

East Asian (EAS) AF: 0.485 AC: 2513 AN: 5182

South Asian (SAS) AF: 0.451 AC: 2170 AN: 4812

European-Finnish (FIN) AF: 0.292 AC: 3082 AN: 10550

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.293 AC: 19918 AN: 67946

Other (OTH) AF: 0.268 AC: 564 AN: 2104

Alfa AF: 0.274 Hom.: 3603

Bravo AF: 0.256

Asia WGS AF: 0.436 AC: 1514 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	5.1
DANN	Benign	0.67
PhyloP100		0.066

Splicing

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

Other links and lift over

dbSNP: rs867177; hg19: chr7-35561870;