rs2215448

chr7-116523898-A-Gchr7-116523898-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 0.846 in 151,602 control chromosomes in the GnomAD database, including 54,407 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 0.85 (54407 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.925 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: 0.846 AC: 128200 AN: 151486 Hom.: 54365 Cov.: 30

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.872

Gnomad EAS AF: 0.947

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.879

Gnomad MID AF: 0.783

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.849

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

GnomAD4 genome AF: 0.846 AC: 128300 AN: 151602 Hom.: 54407 Cov.: 30 AF XY: 0.849 AC XY: 62850 AN XY: 74026

Gnomad4 AFR AF: 0.817

Gnomad4 AMR AF: 0.868

Gnomad4 ASJ AF: 0.872

Gnomad4 EAS AF: 0.947

Gnomad4 SAS AF: 0.864

Gnomad4 FIN AF: 0.879

Gnomad4 NFE AF: 0.844

Gnomad4 OTH AF: 0.849

Alfa AF: 0.849 Hom.: 8205

Bravo AF: 0.845

Asia WGS AF: 0.890 AC: 3090 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	1.8
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2215448; hg19: chr7-116163952;