7-97793614-G-T

Variant names:

• chr7-97793614-G-T
• rs1229542

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 0.204 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.203 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

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.0576

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.170

Alfa AF: 0.142 Hom.: 3251

Bravo AF: 0.215

Asia WGS AF: 0.105 AC: 365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1229542; hg19: chr7-97422926;