chr7-93411158-A-G

Variant names:

• chr7-93411158-A-G
• rs2023778

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 0.378 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.548 AC: 22693 AN: 41448

American (AMR) AF: 0.425 AC: 6489 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1098 AN: 3470

East Asian (EAS) AF: 0.858 AC: 4425 AN: 5158

South Asian (SAS) AF: 0.494 AC: 2378 AN: 4810

European-Finnish (FIN) AF: 0.241 AC: 2549 AN: 10590

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16752 AN: 67942

Other (OTH) AF: 0.383 AC: 807 AN: 2108

Alfa AF: 0.299 Hom.: 24840

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2023778; hg19: chr7-93040470;