7-93411158-A-G

Position:

• chr7-93411158-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 0.378 in 151,996 control chromosomes in the GnomAD database, including 13,016 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 0.38 (13016 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.837 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: 0.378 AC: 57439 AN: 151878 Hom.: 12995 Cov.: 32

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.378 AC: 57512 AN: 151996 Hom.: 13016 Cov.: 32 AF XY: 0.386 AC XY: 28650 AN XY: 74298

Gnomad4 AFR AF: 0.548

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.858

Gnomad4 SAS AF: 0.494

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.383

Alfa AF: 0.280 Hom.: 13538

Bravo AF: 0.401

Asia WGS AF: 0.673 AC: 2338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2023778; hg19: chr7-93040470;