chr2-19689466-C-T

Variant names:

• chr2-19689466-C-T
• rs6531193
• XR_007086240.1:n.392+15307G>A

Variant summary

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

The XR_007086240.1(LOC124905977):​n.392+15307G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 151,982 control chromosomes in the GnomAD database, including 15,640 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 0.44 (15640 hom., cov: 31)
• Consequence: LOC124905977 XR_007086240.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149
• Publications: 2 publications found

Genes affected

LOC124905977 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.495 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: 0.443 AC: 67272 AN: 151862 Hom.: 15637 Cov.: 31

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.0729

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.443 AC: 67295 AN: 151982 Hom.: 15640 Cov.: 31 AF XY: 0.436 AC XY: 32392 AN XY: 74306

African (AFR) AF: 0.396 AC: 16394 AN: 41438

American (AMR) AF: 0.429 AC: 6561 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.560 AC: 1944 AN: 3470

East Asian (EAS) AF: 0.0729 AC: 376 AN: 5158

South Asian (SAS) AF: 0.437 AC: 2099 AN: 4804

European-Finnish (FIN) AF: 0.405 AC: 4287 AN: 10584

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33913 AN: 67934

Other (OTH) AF: 0.464 AC: 979 AN: 2110

Alfa AF: 0.486 Hom.: 12979

Bravo AF: 0.438

Asia WGS AF: 0.256 AC: 897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.52
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs6531193; hg19: chr2-19889227;