XR_007066375.1:n.66+68067C>A

Variant names:

• chr18-53675318-G-T
• rs1442076
• XR_007066375.1:n.66+68067C>A

Variant summary

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

The XR_007066375.1(LOC124904304):​n.66+68067C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 151,660 control chromosomes in the GnomAD database, including 12,257 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 0.40 (12257 hom., cov: 31)
• Consequence: LOC124904304 XR_007066375.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.262
• Publications: 1 publications found

Genes affected

LOC124904304 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60352 AN: 151544 Hom.: 12228 Cov.: 31

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.398 AC: 60417 AN: 151660 Hom.: 12257 Cov.: 31 AF XY: 0.403 AC XY: 29864 AN XY: 74100

African (AFR) AF: 0.414 AC: 17121 AN: 41382

American (AMR) AF: 0.493 AC: 7499 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1469 AN: 3470

East Asian (EAS) AF: 0.478 AC: 2463 AN: 5156

South Asian (SAS) AF: 0.509 AC: 2449 AN: 4808

European-Finnish (FIN) AF: 0.375 AC: 3947 AN: 10518

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.356 AC: 24166 AN: 67804

Other (OTH) AF: 0.401 AC: 844 AN: 2106

Alfa AF: 0.400 Hom.: 2204

Bravo AF: 0.408

Asia WGS AF: 0.475 AC: 1652 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.24
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs1442076; hg19: chr18-51201688;