12-6444664-TG-T

Position:

• chr12-6444664-TG-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NR_015382.2(CD27-AS1):​n.1517-948del variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.28 (1676 hom., cov: 0)
• Consequence: CD27-AS1 NR_015382.2 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.06

Genes affected

CD27-AS1 (HGNC:43896): (CD27 antisense RNA 1)

CD27 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 12-6444664-TG-T is Benign according to our data. Variant chr12-6444664-TG-T is described in ClinVar as [Benign]. Clinvar id is 1256950.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD27-AS1	NR_015382.2	n.1517-948del		intron_variant, non_coding_transcript_variant
CD27	NM_001413266.1	c.-315+554del		intron_variant			NP_001400195.1
CD27	NM_001413267.1	c.-403+554del		intron_variant			NP_001400196.1
CD27	NM_001413268.1	c.-315+66del		intron_variant			NP_001400197.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD27-AS1	ENST00000689782.1	n.460-948del		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.279 AC: 19760 AN: 70918 Hom.: 1679 Cov.: 0

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.260

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.253

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.278 AC: 19748 AN: 70932 Hom.: 1676 Cov.: 0 AF XY: 0.277 AC XY: 8970 AN XY: 32380

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.252

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 18, 2021

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs57782770; hg19: chr12-6553830;