11-19213607-G-T

Variant summary

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

The NR_183675.1(CSRP3-AS1):n.207+16688G>T 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 0.113 in 152,128 control chromosomes in the GnomAD database, including 1,093 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 0.11 (1093 hom., cov: 32)
• Consequence: CSRP3-AS1 NR_183675.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.373

Genes affected

CSRP3-AS1 (HGNC:54183): (CSRP3 and E2F8 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSRP3-AS1	NR_183675.1	n.207+16688G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSRP3-AS1	ENST00000527978.1	n.146-11227G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17264 AN: 152008 Hom.: 1093 Cov.: 32

Gnomad AFR AF: 0.0860

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.0756

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.0909

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.113 AC: 17263 AN: 152128 Hom.: 1093 Cov.: 32 AF XY: 0.114 AC XY: 8476 AN XY: 74382

Gnomad4 AFR AF: 0.0859

Gnomad4 AMR AF: 0.0755

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.0905

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.109

Alfa AF: 0.114 Hom.: 1233

Bravo AF: 0.108

Asia WGS AF: 0.133 AC: 460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.1
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12146588; hg19: chr11-19235154;