rs4266492

Variant names:

• chr6-40727415-A-C
• rs4266492
• XR_926787.3:n.*144A>C

Variant summary

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

The XR_926787.3(LOC105375052):​n.*144A>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0524 in 152,272 control chromosomes in the GnomAD database, including 288 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 0.052 (288 hom., cov: 33)
• Consequence: LOC105375052 XR_926787.3 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.976
• Publications: 1 publications found

Genes affected

LOC105375052 (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 = 0.138 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: 0.0524 AC: 7977 AN: 152154 Hom.: 288 Cov.: 33

Gnomad AFR AF: 0.0250

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0486

Gnomad ASJ AF: 0.0562

Gnomad EAS AF: 0.0702

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.0672

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0592

Gnomad OTH AF: 0.0626

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

GnomAD4 genome AF: 0.0524 AC: 7975 AN: 152272 Hom.: 288 Cov.: 33 AF XY: 0.0542 AC XY: 4034 AN XY: 74458

African (AFR) AF: 0.0250 AC: 1041 AN: 41558

American (AMR) AF: 0.0485 AC: 742 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0562 AC: 195 AN: 3470

East Asian (EAS) AF: 0.0698 AC: 362 AN: 5188

South Asian (SAS) AF: 0.147 AC: 707 AN: 4824

European-Finnish (FIN) AF: 0.0672 AC: 712 AN: 10602

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0592 AC: 4025 AN: 68012

Other (OTH) AF: 0.0619 AC: 131 AN: 2116

Alfa AF: 0.0568 Hom.: 148

Bravo AF: 0.0474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.068
DANN	Benign	0.50
PhyloP100		-0.98

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4266492;

hg19: chr6-40695154;