7-97793614-G-T

Variant names:

• chr7-97793614-G-T
• rs1229542

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 0.204 in 152,096 control chromosomes in the GnomAD database, including 4,200 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 0.20 (4200 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30918 AN: 151978 Hom.: 4199 Cov.: 33

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.0578

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.204 AC: 30954 AN: 152096 Hom.: 4200 Cov.: 33 AF XY: 0.200 AC XY: 14836 AN XY: 74352

African (AFR) AF: 0.397 AC: 16476 AN: 41478

American (AMR) AF: 0.137 AC: 2086 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 463 AN: 3468

East Asian (EAS) AF: 0.101 AC: 521 AN: 5176

South Asian (SAS) AF: 0.0576 AC: 278 AN: 4826

European-Finnish (FIN) AF: 0.138 AC: 1465 AN: 10580

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9052 AN: 67986

Other (OTH) AF: 0.170 AC: 359 AN: 2112

Alfa AF: 0.154 Hom.: 8003

Bravo AF: 0.215

Asia WGS AF: 0.105 AC: 365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.67
PhyloP100		-0.032

Splicing

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

Other links and lift over

dbSNP: rs1229542; hg19: chr7-97422926;