rs2215448

Variant names:

• chr7-116523898-A-G
• rs2215448

Your query was ambiguous. Multiple possible variants found:

• chr7-116523898-A-G
• chr7-116523898-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.817 AC: 33779 AN: 41352

American (AMR) AF: 0.868 AC: 13250 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.872 AC: 3026 AN: 3470

East Asian (EAS) AF: 0.947 AC: 4894 AN: 5168

South Asian (SAS) AF: 0.864 AC: 4150 AN: 4802

European-Finnish (FIN) AF: 0.879 AC: 9056 AN: 10308

Middle Eastern (MID) AF: 0.777 AC: 227 AN: 292

European-Non Finnish (NFE) AF: 0.844 AC: 57364 AN: 67934

Other (OTH) AF: 0.849 AC: 1787 AN: 2106

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
PhyloP100		-0.084

Splicing

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

Other links and lift over

dbSNP: rs2215448; hg19: chr7-116163952;