XR_007065075.1:n.516-633C>T

Variant names:

• chr16-55654572-G-A
• rs1362621
• XR_007065075.1:n.516-633C>T

Variant summary

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

The XR_007065075.1(LOC124903693):​n.516-633C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.748 in 152,122 control chromosomes in the GnomAD database, including 42,783 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 0.75 (42783 hom., cov: 32)
• Consequence: LOC124903693 XR_007065075.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.451
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.8 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: 0.748 AC: 113717 AN: 152004 Hom.: 42746 Cov.: 32

Gnomad AFR AF: 0.807

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.782

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.748 AC: 113818 AN: 152122 Hom.: 42783 Cov.: 32 AF XY: 0.752 AC XY: 55925 AN XY: 74384

African (AFR) AF: 0.807 AC: 33491 AN: 41486

American (AMR) AF: 0.783 AC: 11964 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.707 AC: 2455 AN: 3472

East Asian (EAS) AF: 0.711 AC: 3670 AN: 5164

South Asian (SAS) AF: 0.728 AC: 3506 AN: 4814

European-Finnish (FIN) AF: 0.737 AC: 7799 AN: 10586

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.715 AC: 48600 AN: 67992

Other (OTH) AF: 0.734 AC: 1551 AN: 2114

Alfa AF: 0.749 Hom.: 11958

Bravo AF: 0.755

Asia WGS AF: 0.715 AC: 2485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.56
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs1362621; hg19: chr16-55688484;