chr7-116522675-G-A

Position:

• chr7-116522675-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 0.274 in 152,128 control chromosomes in the GnomAD database, including 6,358 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 0.27 (6358 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.353

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.366 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: 0.274 AC: 41718 AN: 152010 Hom.: 6356 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.0114

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.274 AC: 41744 AN: 152128 Hom.: 6358 Cov.: 32 AF XY: 0.264 AC XY: 19658 AN XY: 74380

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.0114

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.291

Alfa AF: 0.270 Hom.: 8547

Bravo AF: 0.287

Asia WGS AF: 0.0990 AC: 347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.2
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4236601; hg19: chr7-116162729;