rs7248320

Positions:

• chr19-48256972-G-A
• chr19-48256972-G-C

Variant summary

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

The ENST00000602172.1(CARD8-AS1):​n.742G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.647 in 152,026 control chromosomes in the GnomAD database, including 31,955 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 0.65 (31955 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: CARD8-AS1 ENST00000602172.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

Genes affected

CARD8-AS1 (HGNC:51408): (CARD8 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CARD8-AS1	NR_040599.1	n.742G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CARD8-AS1	ENST00000602172.1	n.742G>A		non_coding_transcript_exon_variant	2/2	1

Frequencies

GnomAD3 genomes AF: 0.647 AC: 98213 AN: 151908 Hom.: 31919 Cov.: 32

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.659

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.647 AC: 98300 AN: 152026 Hom.: 31955 Cov.: 32 AF XY: 0.644 AC XY: 47826 AN XY: 74316

Gnomad4 AFR AF: 0.707

Gnomad4 AMR AF: 0.668

Gnomad4 ASJ AF: 0.706

Gnomad4 EAS AF: 0.665

Gnomad4 SAS AF: 0.697

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.664

Alfa AF: 0.634 Hom.: 51551

Bravo AF: 0.659

Asia WGS AF: 0.713 AC: 2480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.2
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7248320; hg19: chr19-48760229;