rs7614488

Variant names:

• chr3-106302653-T-C
• rs7614488
• XR_001740840.1:n.82+1537A>G

Variant summary

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

The XR_001740840.1(LOC107986112):​n.82+1537A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.811 in 151,976 control chromosomes in the GnomAD database, including 52,015 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 0.81 (52015 hom., cov: 31)
• Consequence: LOC107986112 XR_001740840.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174
• Publications: 3 publications found

Genes affected

LOC107986112 (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 (NFE) allele frequency at 95% confidence interval = 0.93 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: 0.811 AC: 123234 AN: 151860 Hom.: 51995 Cov.: 31

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.867

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.833

Gnomad FIN AF: 0.929

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.936

Gnomad OTH AF: 0.830

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

GnomAD4 genome AF: 0.811 AC: 123296 AN: 151976 Hom.: 52015 Cov.: 31 AF XY: 0.811 AC XY: 60256 AN XY: 74288

African (AFR) AF: 0.557 AC: 23063 AN: 41430

American (AMR) AF: 0.853 AC: 12999 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.867 AC: 3006 AN: 3466

East Asian (EAS) AF: 0.775 AC: 3999 AN: 5160

South Asian (SAS) AF: 0.835 AC: 4028 AN: 4826

European-Finnish (FIN) AF: 0.929 AC: 9849 AN: 10604

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.936 AC: 63577 AN: 67938

Other (OTH) AF: 0.830 AC: 1750 AN: 2108

Alfa AF: 0.889 Hom.: 200129

Bravo AF: 0.793

Asia WGS AF: 0.805 AC: 2798 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	1.2
DANN	Benign	0.84
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs7614488; hg19: chr3-106021500;