rs11873656

Positions:

• chr18-24751801-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_134604.1(LOC105372028):​n.308-14680A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,032 control chromosomes in the GnomAD database, including 7,207 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 0.30 (7207 hom., cov: 32)
• Consequence: LOC105372028 NR_134604.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372028	NR_134604.1	n.308-14680A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000654065.1	n.226+25044A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45630 AN: 151914 Hom.: 7201 Cov.: 32

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.300 AC: 45674 AN: 152032 Hom.: 7207 Cov.: 32 AF XY: 0.306 AC XY: 22714 AN XY: 74310

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.442

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.323

Alfa AF: 0.268 Hom.: 899

Bravo AF: 0.308

Asia WGS AF: 0.388 AC: 1351 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.19
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11873656; hg19: chr18-22331765;