7-113088855-G-A

Position:

• chr7-113088855-G-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 0.29 in 151,918 control chromosomes in the GnomAD database, including 7,923 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 0.29 (7923 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.498 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: 0.290 AC: 43947 AN: 151798 Hom.: 7908 Cov.: 32

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.0516

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.290 AC: 43992 AN: 151918 Hom.: 7923 Cov.: 32 AF XY: 0.286 AC XY: 21231 AN XY: 74252

Gnomad4 AFR AF: 0.504

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.0520

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.285

Alfa AF: 0.218 Hom.: 1788

Bravo AF: 0.296

Asia WGS AF: 0.207 AC: 720 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.35
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1575013; hg19: chr7-112728910;