rs848452

Positions:

• chr7-77967495-T-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 0.84 in 152,198 control chromosomes in the GnomAD database, including 54,078 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 0.84 (54078 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.840 AC: 127790 AN: 152080 Hom.: 54062 Cov.: 33

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.900

Gnomad AMR AF: 0.864

Gnomad ASJ AF: 0.896

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.845

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.903

Gnomad OTH AF: 0.859

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

GnomAD4 genome AF: 0.840 AC: 127858 AN: 152198 Hom.: 54078 Cov.: 33 AF XY: 0.835 AC XY: 62114 AN XY: 74404

Gnomad4 AFR AF: 0.733

Gnomad4 AMR AF: 0.864

Gnomad4 ASJ AF: 0.896

Gnomad4 EAS AF: 0.832

Gnomad4 SAS AF: 0.727

Gnomad4 FIN AF: 0.845

Gnomad4 NFE AF: 0.903

Gnomad4 OTH AF: 0.856

Alfa AF: 0.891 Hom.: 79934

Bravo AF: 0.842

Asia WGS AF: 0.769 AC: 2674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs848452; hg19: chr7-77596812;