7-47703658-A-G

Variant names:

• chr7-47703658-A-G
• rs7791862

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 0.184 in 152,232 control chromosomes in the GnomAD database, including 3,079 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 0.18 (3079 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.349 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: 0.184 AC: 28054 AN: 152112 Hom.: 3082 Cov.: 32

Gnomad AFR AF: 0.0620

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.208

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.184 AC: 28060 AN: 152232 Hom.: 3079 Cov.: 32 AF XY: 0.187 AC XY: 13922 AN XY: 74422

Gnomad4 AFR AF: 0.0619

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.363

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.172

Alfa AF: 0.141 Hom.: 357

Bravo AF: 0.185

Asia WGS AF: 0.262 AC: 911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7791862; hg19: chr7-47743256;