rs11872889

chr18-60350190-G-A

Variant summary

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

The ENST00000658928.1(ENSG00000285681):n.156+20845G>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 0.0352 in 152,240 control chromosomes in the GnomAD database, including 142 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 0.035 (142 hom., cov: 32)
• Consequence: ENST00000658928.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0545 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+20845G>A		intron_variant, non_coding_transcript_variant
	ENST00000650201.1	n.113+20845G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0352 AC: 5358 AN: 152122 Hom.: 142 Cov.: 32

Gnomad AFR AF: 0.00956

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0365

Gnomad ASJ AF: 0.0643

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.00580

Gnomad FIN AF: 0.0188

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0560

Gnomad OTH AF: 0.0474

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

GnomAD4 genome AF: 0.0352 AC: 5355 AN: 152240 Hom.: 142 Cov.: 32 AF XY: 0.0319 AC XY: 2378 AN XY: 74444

Gnomad4 AFR AF: 0.00951

Gnomad4 AMR AF: 0.0364

Gnomad4 ASJ AF: 0.0643

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.00581

Gnomad4 FIN AF: 0.0188

Gnomad4 NFE AF: 0.0560

Gnomad4 OTH AF: 0.0469

Alfa AF: 0.0487 Hom.: 36

Bravo AF: 0.0362

Asia WGS AF: 0.00751 AC: 26 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	2.8
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11872889; hg19: chr18-58017423;