rs7456706

Positions:

• chr7-118029908-C-A

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 0.15 in 152,110 control chromosomes in the GnomAD database, including 1,935 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 0.15 (1935 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.258

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.196 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: 0.150 AC: 22867 AN: 151990 Hom.: 1938 Cov.: 32

Gnomad AFR AF: 0.0859

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.0817

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.150 AC: 22858 AN: 152110 Hom.: 1935 Cov.: 32 AF XY: 0.145 AC XY: 10749 AN XY: 74334

Gnomad4 AFR AF: 0.0857

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.153

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.0820

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.168

Alfa AF: 0.190 Hom.: 3413

Bravo AF: 0.149

Asia WGS AF: 0.107 AC: 372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.2
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7456706; hg19: chr7-117669962;