7-117977865-C-T

Position:

• chr7-117977865-C-T

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 0.345 in 152,066 control chromosomes in the GnomAD database, including 10,269 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 0.35 (10269 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.233

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.424 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: 0.346 AC: 52504 AN: 151948 Hom.: 10275 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.345 AC: 52508 AN: 152066 Hom.: 10269 Cov.: 32 AF XY: 0.353 AC XY: 26209 AN XY: 74350

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.549

Gnomad4 NFE AF: 0.428

Gnomad4 OTH AF: 0.328

Alfa AF: 0.413 Hom.: 6057

Bravo AF: 0.314

Asia WGS AF: 0.306 AC: 1065 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.9
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7793280; hg19: chr7-117617919;