7-35522260-T-C

Position:

• chr7-35522260-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.268

Alfa AF: 0.273 Hom.: 3268

Bravo AF: 0.256

Asia WGS AF: 0.436 AC: 1514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.1
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs867177; hg19: chr7-35561870;