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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375052	XR_926787.3	n.*144A>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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

Other links and lift over

dbSNP: rs4266492; hg19: chr6-40695154;