XR_007065075.1:n.515+424G>C

Variant names:

• chr16-55655175-C-G
• rs2397771
• XR_007065075.1:n.515+424G>C

Variant summary

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

The XR_007065075.1(LOC124903693):​n.515+424G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 152,080 control chromosomes in the GnomAD database, including 29,318 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 0.62 (29318 hom., cov: 32)
• Consequence: LOC124903693 XR_007065075.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.327
• Publications: 8 publications found

Genes affected

LOC124903693 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.683 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: 0.620 AC: 94183 AN: 151962 Hom.: 29293 Cov.: 32

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.620 AC: 94266 AN: 152080 Hom.: 29318 Cov.: 32 AF XY: 0.623 AC XY: 46278 AN XY: 74340

African (AFR) AF: 0.649 AC: 26925 AN: 41486

American (AMR) AF: 0.647 AC: 9891 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.598 AC: 2076 AN: 3472

East Asian (EAS) AF: 0.684 AC: 3531 AN: 5162

South Asian (SAS) AF: 0.702 AC: 3377 AN: 4808

European-Finnish (FIN) AF: 0.561 AC: 5936 AN: 10578

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.596 AC: 40507 AN: 67976

Other (OTH) AF: 0.625 AC: 1317 AN: 2108

Alfa AF: 0.471 Hom.: 1124

Bravo AF: 0.642

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.1
DANN	Benign	0.37
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs2397771; hg19: chr16-55689087;