rs7248320

Variant names:

• chr19-48256972-G-A
• rs7248320
• ENST00000602172.1:n.742G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000602172.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CARD8-AS1	NR_040599.1		n.742G>A		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CARD8-AS1	ENST00000602172.1	TSL:1	n.742G>A		non_coding_transcript_exon	Exon 2 of 2

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

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) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.707 AC: 29313 AN: 41466

American (AMR) AF: 0.668 AC: 10206 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2450 AN: 3470

East Asian (EAS) AF: 0.665 AC: 3440 AN: 5174

South Asian (SAS) AF: 0.697 AC: 3360 AN: 4824

European-Finnish (FIN) AF: 0.495 AC: 5212 AN: 10530

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.620 AC: 42150 AN: 67986

Other (OTH) AF: 0.664 AC: 1399 AN: 2108

Alfa AF: 0.639 Hom.: 86850

Bravo AF: 0.659

Asia WGS AF: 0.713 AC: 2480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.2
DANN	Benign	0.85
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7248320;

hg19: chr19-48760229;