rs7789940

chr7-76321913-A-Gchr7-76321913-A-T

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 0.3 in 152,010 control chromosomes in the GnomAD database, including 6,989 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 0.30 (6989 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45515 AN: 151892 Hom.: 6983 Cov.: 31

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.300 AC: 45530 AN: 152010 Hom.: 6989 Cov.: 31 AF XY: 0.303 AC XY: 22525 AN XY: 74306

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.440

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.282

Alfa AF: 0.289 Hom.: 8675

Bravo AF: 0.302

Asia WGS AF: 0.342 AC: 1194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	1.0
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7789940; hg19: chr7-75951230;