rs11241130

Positions:

• chr5-111623085-G-A
• chr5-111623085-G-C
• chr5-111623085-G-T

Variant summary

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

The NR_040093.1(STARD4-AS1):​n.284-46334G>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 0.798 in 151,972 control chromosomes in the GnomAD database, including 50,531 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 0.80 (50531 hom., cov: 32)
• Consequence: STARD4-AS1 NR_040093.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610

Genes affected

STARD4-AS1 (HGNC:44117): (STARD4 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.918 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STARD4-AS1	NR_040093.1	n.284-46334G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STARD4-AS1	ENST00000500779.2	n.284-46334G>A		intron_variant, non_coding_transcript_variant		1
STARD4-AS1	ENST00000666013.1	n.2114-46334G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121182 AN: 151854 Hom.: 50516 Cov.: 32

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.974

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.867

Gnomad EAS AF: 0.798

Gnomad SAS AF: 0.745

Gnomad FIN AF: 0.927

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.924

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.798 AC: 121241 AN: 151972 Hom.: 50531 Cov.: 32 AF XY: 0.798 AC XY: 59305 AN XY: 74320

Gnomad4 AFR AF: 0.533

Gnomad4 AMR AF: 0.854

Gnomad4 ASJ AF: 0.867

Gnomad4 EAS AF: 0.798

Gnomad4 SAS AF: 0.746

Gnomad4 FIN AF: 0.927

Gnomad4 NFE AF: 0.924

Gnomad4 OTH AF: 0.806

Alfa AF: 0.904 Hom.: 97904

Bravo AF: 0.781

Asia WGS AF: 0.780 AC: 2697 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11241130; hg19: chr5-110958782;