rs917836

Positions:

• chr18-22473405-A-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC124904260 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904260	XR_007066305.1	n.2366T>A		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0395

Gnomad4 AMR AF: 0.0436

Gnomad4 ASJ AF: 0.0513

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0880

Gnomad4 FIN AF: 0.0712

Gnomad4 NFE AF: 0.0606

Gnomad4 OTH AF: 0.0530

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs917836; hg19: chr18-20053368;