rs2881814

Variant names:

• chr7-7324759-A-G
• rs2881814
• XR_002956539.2:n.442-51802A>G

Your query was ambiguous. Multiple possible variants found:

• chr7-7324759-A-G
• chr7-7324759-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_002956539.2(LOC107986764):​n.442-51802A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.742 in 152,100 control chromosomes in the GnomAD database, including 42,673 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 0.74 (42673 hom., cov: 32)
• Consequence: LOC107986764 XR_002956539.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.479
• Publications: 1 publications found

Genes affected

LOC107986764 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.86 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.742 AC: 112839 AN: 151982 Hom.: 42641 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.832

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.756

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.820

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.742 AC: 112924 AN: 152100 Hom.: 42673 Cov.: 32 AF XY: 0.750 AC XY: 55780 AN XY: 74350

African (AFR) AF: 0.598 AC: 24798 AN: 41454

American (AMR) AF: 0.800 AC: 12239 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.756 AC: 2621 AN: 3468

East Asian (EAS) AF: 0.879 AC: 4535 AN: 5160

South Asian (SAS) AF: 0.882 AC: 4252 AN: 4820

European-Finnish (FIN) AF: 0.820 AC: 8672 AN: 10576

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.783 AC: 53260 AN: 68014

Other (OTH) AF: 0.746 AC: 1578 AN: 2114

Alfa AF: 0.758 Hom.: 7702

Bravo AF: 0.731

Asia WGS AF: 0.886 AC: 3081 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.52
DANN	Benign	0.70
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs2881814; hg19: chr7-7364390;