XR_007059730.1:n.6421C>A

Variant names:

• chr6-119873770-C-A
• rs937091
• XR_007059730.1:n.6421C>A

Variant summary

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

The XR_007059730.1(LOC124901390):​n.6421C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 151,460 control chromosomes in the GnomAD database, including 18,637 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 0.49 (18637 hom., cov: 31)
• Consequence: LOC124901390 XR_007059730.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.863
• Publications: 3 publications found

Genes affected

LOC124901390 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.617 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: 0.489 AC: 74046 AN: 151342 Hom.: 18630 Cov.: 31

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.489 AC: 74091 AN: 151460 Hom.: 18637 Cov.: 31 AF XY: 0.486 AC XY: 35967 AN XY: 73966

African (AFR) AF: 0.596 AC: 24652 AN: 41354

American (AMR) AF: 0.368 AC: 5590 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1539 AN: 3462

East Asian (EAS) AF: 0.635 AC: 3243 AN: 5104

South Asian (SAS) AF: 0.436 AC: 2096 AN: 4808

European-Finnish (FIN) AF: 0.497 AC: 5221 AN: 10504

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.447 AC: 30277 AN: 67750

Other (OTH) AF: 0.471 AC: 991 AN: 2106

Alfa AF: 0.456 Hom.: 8072

Bravo AF: 0.489

Asia WGS AF: 0.496 AC: 1723 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.28
DANN	Benign	0.50
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs937091; hg19: chr6-120194916;