XR_001739572.1:n.72-12734T>C

Variant names:

• chr2-84217762-A-G
• rs6547537
• XR_001739572.1:n.72-12734T>C

Variant summary

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

The XR_001739572.1(LOC107985905):​n.72-12734T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.706 in 152,034 control chromosomes in the GnomAD database, including 38,895 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 0.71 (38895 hom., cov: 32)
• Consequence: LOC107985905 XR_001739572.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303
• Publications: 7 publications found

Genes affected

LOC107985905 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.706 AC: 107230 AN: 151916 Hom.: 38863 Cov.: 32

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.753

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.802

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.771

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.706 AC: 107310 AN: 152034 Hom.: 38895 Cov.: 32 AF XY: 0.712 AC XY: 52926 AN XY: 74334

African (AFR) AF: 0.518 AC: 21452 AN: 41410

American (AMR) AF: 0.754 AC: 11525 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.808 AC: 2803 AN: 3470

East Asian (EAS) AF: 0.886 AC: 4579 AN: 5168

South Asian (SAS) AF: 0.803 AC: 3867 AN: 4816

European-Finnish (FIN) AF: 0.777 AC: 8224 AN: 10578

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.771 AC: 52404 AN: 67980

Other (OTH) AF: 0.730 AC: 1541 AN: 2112

Alfa AF: 0.676 Hom.: 17056

Bravo AF: 0.695

Asia WGS AF: 0.811 AC: 2819 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.8
DANN	Benign	0.38
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs6547537; hg19: chr2-84444886;