rs1648234

Positions:

• chr11-19308167-G-A

Variant summary

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

The NR_183675.1(CSRP3-AS1):​n.623-23G>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 0.711 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 NR_183675.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.503

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
CSRP3-AS1	NR_183675.1	n.623-23G>A		intron_variant, non_coding_transcript_variant
CSRP3-AS1	NR_183672.1	n.1000-23G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000528326.5	n.480-23G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000529082.1	n.254-23G>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 NFE exome AF: 0.875

Gnomad4 OTH exome AF: 1.00

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

Gnomad4 AFR AF: 0.839

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.650

Gnomad4 EAS AF: 0.432

Gnomad4 SAS AF: 0.625

Gnomad4 FIN AF: 0.705

Gnomad4 NFE AF: 0.691

Gnomad4 OTH AF: 0.682

Alfa AF: 0.698 Hom.: 6344

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1648234; hg19: chr11-19329714;