7-113088952-A-G

Position:

• chr7-113088952-A-G

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 0.327 in 152,000 control chromosomes in the GnomAD database, including 8,684 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 0.33 (8684 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990

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 (NFE) allele frequency at 95% confidence interval = 0.393 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: 0.327 AC: 49636 AN: 151882 Hom.: 8678 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.0484

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.327 AC: 49668 AN: 152000 Hom.: 8684 Cov.: 32 AF XY: 0.322 AC XY: 23932 AN XY: 74306

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.331

Gnomad4 ASJ AF: 0.462

Gnomad4 EAS AF: 0.0482

Gnomad4 SAS AF: 0.290

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.397

Gnomad4 OTH AF: 0.368

Alfa AF: 0.348 Hom.: 1466

Bravo AF: 0.321

Asia WGS AF: 0.214 AC: 743 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.57
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12705846; hg19: chr7-112729007;