rs6518322

chr21-43805987-A-Gchr21-43805987-A-T

Variant summary

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

The NR_026961.1(AATBC):n.4369T>C 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 0.573 in 151,958 control chromosomes in the GnomAD database, including 26,971 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 0.57 (26960 hom., cov: 31)
  • Exomes 𝑓: 0.56 (11 hom.)
• Consequence: AATBC NR_026961.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.134

Genes affected

AATBC (HGNC:51526): (apoptosis associated transcript in bladder cancer)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AATBC	NR_026961.1	n.4369T>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AATBC	ENST00000400385.2	n.4369T>C		non_coding_transcript_exon_variant	2/2	2
AATBC	ENST00000437258.5	n.703T>C		non_coding_transcript_exon_variant	2/2	1
AATBC	ENST00000448247.5	n.1660T>C		non_coding_transcript_exon_variant	4/4	2

Frequencies

GnomAD3 genomes AF: 0.573 AC: 86953 AN: 151768 Hom.: 26914 Cov.: 31

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.619

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.770

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.559

GnomAD4 exome AF: 0.556 AC: 40 AN: 72 Hom.: 11 Cov.: 0 AF XY: 0.500 AC XY: 14 AN XY: 28

Gnomad4 FIN exome AF: 0.603

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.573 AC: 87056 AN: 151886 Hom.: 26960 Cov.: 31 AF XY: 0.580 AC XY: 43040 AN XY: 74242

Gnomad4 AFR AF: 0.777

Gnomad4 AMR AF: 0.641

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.771

Gnomad4 SAS AF: 0.727

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.565

Alfa AF: 0.527 Hom.: 3874

Bravo AF: 0.595

Asia WGS AF: 0.751 AC: 2612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	2.5
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6518322; hg19: chr21-45225868;