ENST00000527978.2:n.708-23G>A

Variant names:

• chr11-19308167-G-A
• rs1648234
• ENST00000527978.2:n.708-23G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000527978.2(CSRP3-AS1):​n.708-23G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 152,034 control chromosomes in the GnomAD database, including 39,181 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 0.71 (39177 hom., cov: 31)
  • Exomes 𝑓: 0.90 (4 hom.)
• Consequence: CSRP3-AS1 ENST00000527978.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.503
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.831 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSRP3-AS1	NR_183672.1	n.1000-23G>A		intron_variant	Intron 5 of 6
CSRP3-AS1	NR_183675.1	n.623-23G>A		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSRP3-AS1	ENST00000527978.2	n.708-23G>A		intron_variant	Intron 5 of 6	5
CSRP3-AS1	ENST00000529082.1	n.254-23G>A		intron_variant	Intron 2 of 2	5
CSRP3-AS1	ENST00000718486.1	n.480-23G>A		intron_variant	Intron 3 of 3
CSRP3-AS1	ENST00000850663.1	n.595-23G>A		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.711 AC: 107991 AN: 151908 Hom.: 39143 Cov.: 31

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.685

GnomAD4 exome AF: 0.900 AC: 9 AN: 10 Hom.: 4 Cov.: 0 AF XY: 1.00 AC XY: 8 AN XY: 8

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.875 AC: 7 AN: 8

Other (OTH) AF: 1.00 AC: 2 AN: 2

GnomAD4 genome AF: 0.711 AC: 108087 AN: 152024 Hom.: 39177 Cov.: 31 AF XY: 0.706 AC XY: 52463 AN XY: 74288

African (AFR) AF: 0.839 AC: 34815 AN: 41506

American (AMR) AF: 0.608 AC: 9287 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 2253 AN: 3468

East Asian (EAS) AF: 0.432 AC: 2223 AN: 5146

South Asian (SAS) AF: 0.625 AC: 3007 AN: 4810

European-Finnish (FIN) AF: 0.705 AC: 7438 AN: 10556

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.691 AC: 46968 AN: 67946

Other (OTH) AF: 0.682 AC: 1440 AN: 2110

Alfa AF: 0.701 Hom.: 6612

Bravo AF: 0.701

Asia WGS AF: 0.574 AC: 1997 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.26
DANN	Benign	0.67
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs1648234; hg19: chr11-19329714;