4-86924979-C-T

Variant summary

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

The NR_038841.1(AFF1-AS1):n.1860G>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 0.409 in 152,016 control chromosomes in the GnomAD database, including 15,371 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 0.41 (15368 hom., cov: 32)
  • Exomes 𝑓: 0.54 (3 hom.)
• Consequence: AFF1-AS1 NR_038841.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AFF1-AS1	NR_038841.1	n.1860G>A		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000508280.6	n.1809G>A		non_coding_transcript_exon_variant	4/4	2

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62224 AN: 151874 Hom.: 15370 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.453

GnomAD4 exome AF: 0.542 AC: 13 AN: 24 Hom.: 3 Cov.: 0 AF XY: 0.500 AC XY: 9 AN XY: 18

Gnomad4 NFE exome AF: 0.542

GnomAD4 genome AF: 0.409 AC: 62227 AN: 151992 Hom.: 15368 Cov.: 32 AF XY: 0.410 AC XY: 30448 AN XY: 74290

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.645

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.578

Gnomad4 FIN AF: 0.456

Gnomad4 NFE AF: 0.543

Gnomad4 OTH AF: 0.453

Alfa AF: 0.333 Hom.: 1023

Bravo AF: 0.395

Asia WGS AF: 0.502 AC: 1746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.3
Dann	Benign	0.68

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2785; hg19: chr4-87846131;