rs7456706

Variant names:

• chr7-118029908-C-A
• rs7456706

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 0.15 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0857 AC: 3557 AN: 41526

American (AMR) AF: 0.131 AC: 2005 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 531 AN: 3468

East Asian (EAS) AF: 0.103 AC: 533 AN: 5166

South Asian (SAS) AF: 0.0820 AC: 394 AN: 4806

European-Finnish (FIN) AF: 0.156 AC: 1651 AN: 10596

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13496 AN: 67960

Other (OTH) AF: 0.168 AC: 354 AN: 2112

Alfa AF: 0.189 Hom.: 3873

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
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs7456706; hg19: chr7-117669962;