rs11872992

Positions:

• chr18-60373354-G-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The ENST00000658928.1(ENSG00000285681):​n.156+44009G>A 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 0.123 in 152,116 control chromosomes in the GnomAD database, including 1,500 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars).

• Frequency: Genomes: 𝑓 0.12 (1500 hom., cov: 32)
• Consequence: ENST00000658928.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 18-60373354-G-A is Benign according to our data. Variant chr18-60373354-G-A is described in Lovd as [Likely_benign].
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000658928.1	n.156+44009G>A		intron_variant, non_coding_transcript_variant
	ENST00000650201.1	n.113+44009G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18680 AN: 151998 Hom.: 1500 Cov.: 32

Gnomad AFR AF: 0.0329

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.123 AC: 18685 AN: 152116 Hom.: 1500 Cov.: 32 AF XY: 0.129 AC XY: 9603 AN XY: 74336

Gnomad4 AFR AF: 0.0328

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.121

Alfa AF: 0.141 Hom.: 2171

Bravo AF: 0.110

Asia WGS AF: 0.172 AC: 594 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.12
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11872992; hg19: chr18-58040587;