rs848452

Variant names:

• chr7-77967495-T-C
• rs848452

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;