rs7792319

Variant names:

• chr7-19127389-G-A
• rs7792319

Your query was ambiguous. Multiple possible variants found:

• chr7-19127389-G-A
• chr7-19127389-G-C

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 0.0641 in 152,148 control chromosomes in the GnomAD database, including 564 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 0.064 (564 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.298

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.182 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: 0.0641 AC: 9744 AN: 152030 Hom.: 562 Cov.: 32

Gnomad AFR AF: 0.0299

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.0329

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.0643

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0487

Gnomad OTH AF: 0.0636

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

GnomAD4 genome AF: 0.0641 AC: 9751 AN: 152148 Hom.: 564 Cov.: 32 AF XY: 0.0706 AC XY: 5246 AN XY: 74354

Gnomad4 AFR AF: 0.0298

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.0329

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.0643

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.0487

Gnomad4 OTH AF: 0.0629

Alfa AF: 0.0692 Hom.: 156

Bravo AF: 0.0660

Asia WGS AF: 0.133 AC: 462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.57
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7792319; hg19: chr7-19167012;