rs917836

Variant names:

• chr18-22473405-A-T
• rs917836
• XR_007066305.1:n.2366T>A

Variant summary

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

The XR_007066305.1(LOC124904260):​n.2366T>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 0.0527 in 152,272 control chromosomes in the GnomAD database, including 214 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 0.053 (214 hom., cov: 32)
• Consequence: LOC124904260 XR_007066305.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.791
• Publications: 4 publications found

Genes affected

LOC124904260 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0811 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: 0.0527 AC: 8022 AN: 152154 Hom.: 213 Cov.: 32

Gnomad AFR AF: 0.0395

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.0436

Gnomad ASJ AF: 0.0513

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0882

Gnomad FIN AF: 0.0712

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0606

Gnomad OTH AF: 0.0540

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

GnomAD4 genome AF: 0.0527 AC: 8019 AN: 152272 Hom.: 214 Cov.: 32 AF XY: 0.0539 AC XY: 4014 AN XY: 74444

African (AFR) AF: 0.0395 AC: 1641 AN: 41554

American (AMR) AF: 0.0436 AC: 667 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0513 AC: 178 AN: 3472

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5174

South Asian (SAS) AF: 0.0880 AC: 425 AN: 4828

European-Finnish (FIN) AF: 0.0712 AC: 755 AN: 10610

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0606 AC: 4124 AN: 68012

Other (OTH) AF: 0.0530 AC: 112 AN: 2114

Alfa AF: 0.0601 Hom.: 35

Bravo AF: 0.0492

Asia WGS AF: 0.0400 AC: 141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.6
DANN	Benign	0.50
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs917836; hg19: chr18-20053368;