rs6518322

Variant names:

• chr21-43805987-A-G
• rs6518322
• ENST00000437258.5:n.703T>C

Your query was ambiguous. Multiple possible variants found:

• chr21-43805987-A-G
• chr21-43805987-A-T

Variant summary

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

The ENST00000437258.5(AATBC):​n.703T>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 ENST00000437258.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.134
• Publications: 9 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
AATBC	NR_026961.1	n.4369T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AATBC	ENST00000437258.5	n.703T>C		non_coding_transcript_exon_variant	Exon 2 of 2	1
AATBC	ENST00000400385.2	n.4369T>C		non_coding_transcript_exon_variant	Exon 2 of 2	2
AATBC	ENST00000448247.5	n.1660T>C		non_coding_transcript_exon_variant	Exon 4 of 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

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) AF: 0.603 AC: 35 AN: 58

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 5 AN: 10

Other (OTH) AF: 0.00 AC: 0 AN: 4

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

African (AFR) AF: 0.777 AC: 32162 AN: 41410

American (AMR) AF: 0.641 AC: 9791 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1658 AN: 3468

East Asian (EAS) AF: 0.771 AC: 3976 AN: 5160

South Asian (SAS) AF: 0.727 AC: 3489 AN: 4796

European-Finnish (FIN) AF: 0.464 AC: 4895 AN: 10552

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29167 AN: 67924

Other (OTH) AF: 0.565 AC: 1192 AN: 2108

Alfa AF: 0.533 Hom.: 4099

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
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs6518322; hg19: chr21-45225868;