rs2868370

Variant names:

• chr7-76301483-G-A
• rs2868370

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 0.156 in 151,592 control chromosomes in the GnomAD database, including 2,048 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 0.16 (2048 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.901

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 (AMR) allele frequency at 95% confidence interval = 0.178 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: 0.156 AC: 23576 AN: 151484 Hom.: 2049 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.0987

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.156 AC: 23574 AN: 151592 Hom.: 2048 Cov.: 32 AF XY: 0.159 AC XY: 11758 AN XY: 73994

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.0987

Gnomad4 EAS AF: 0.183

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.138

Alfa AF: 0.163 Hom.: 256

Bravo AF: 0.148

Asia WGS AF: 0.174 AC: 605 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	4.9
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2868370; hg19: chr7-75930800;