7-106954440-C-T

Position:

• chr7-106954440-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 0.244 in 151,884 control chromosomes in the GnomAD database, including 5,073 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 0.24 (5073 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.404

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37015 AN: 151766 Hom.: 5043 Cov.: 31

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.0642

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.244 AC: 37102 AN: 151884 Hom.: 5073 Cov.: 31 AF XY: 0.241 AC XY: 17855 AN XY: 74230

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.0642

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.214

Alfa AF: 0.214 Hom.: 1727

Bravo AF: 0.248

Asia WGS AF: 0.139 AC: 481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7779057; hg19: chr7-106594885;