rs9348512

Variant names:

• chr6-10456473-C-A
• rs9348512
• ENST00000366312.2:n.348C>A

Variant summary

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

The ENST00000366312.2(TFAP2A-AS1):​n.348C>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 0.339 in 152,156 control chromosomes in the GnomAD database, including 9,056 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 0.34 (9055 hom., cov: 32)
  • Exomes 𝑓: 0.27 (1 hom.)
• Consequence: TFAP2A-AS1 ENST00000366312.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 16 publications found

Genes affected

TFAP2A-AS1 (HGNC:40579): (TFAP2A antisense RNA 1)

MIR5689HG (HGNC:52007): (MIR5689 host gene)

LINC00518 (HGNC:28626): (long intergenic non-protein coding RNA 518)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000366312.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR5689HG	NR_132993.1		n.348C>A		non_coding_transcript_exon	Exon 4 of 4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TFAP2A-AS1	ENST00000366312.2	TSL:3	n.348C>A		non_coding_transcript_exon	Exon 4 of 4
	TFAP2A-AS1	ENST00000742302.1		n.392C>A		non_coding_transcript_exon	Exon 4 of 4
	TFAP2A-AS1	ENST00000742303.1		n.434C>A		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51544 AN: 152016 Hom.: 9058 Cov.: 32

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.328

GnomAD4 exome AF: 0.273 AC: 6 AN: 22 Hom.: 1 Cov.: 0 AF XY: 0.278 AC XY: 5 AN XY: 18

African (AFR) AF: 0.00 AC: 0 AN: 4

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) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.375 AC: 6 AN: 16

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.339 AC: 51582 AN: 152134 Hom.: 9055 Cov.: 32 AF XY: 0.340 AC XY: 25294 AN XY: 74376

African (AFR) AF: 0.335 AC: 13894 AN: 41490

American (AMR) AF: 0.393 AC: 5996 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1275 AN: 3468

East Asian (EAS) AF: 0.183 AC: 947 AN: 5180

South Asian (SAS) AF: 0.540 AC: 2603 AN: 4820

European-Finnish (FIN) AF: 0.290 AC: 3073 AN: 10586

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.335 AC: 22791 AN: 67998

Other (OTH) AF: 0.325 AC: 688 AN: 2114

Alfa AF: 0.339 Hom.: 27920

Bravo AF: 0.340

Asia WGS AF: 0.345 AC: 1200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.9
DANN	Benign	0.73
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs9348512; hg19: chr6-10456706;