rs1217394

chr1-113891037-G-A

Variant summary

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

The NR_125965.1(AP4B1-AS1):n.415-6831G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.758 in 152,180 control chromosomes in the GnomAD database, including 44,769 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 0.76 (44769 hom., cov: 32)
• Consequence: AP4B1-AS1 NR_125965.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

Genes affected

AP4B1-AS1 (HGNC:44114): (AP4B1 antisense RNA 1)

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 (AFR) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AP4B1-AS1	NR_125965.1	n.415-6831G>A		intron_variant, non_coding_transcript_variant
AP4B1-AS1	NR_037864.1	n.247-6831G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AP4B1-AS1	ENST00000419536.1	n.247-6831G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.758 AC: 115245 AN: 152060 Hom.: 44715 Cov.: 32

Gnomad AFR AF: 0.934

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.758 AC: 115357 AN: 152180 Hom.: 44769 Cov.: 32 AF XY: 0.757 AC XY: 56278 AN XY: 74378

Gnomad4 AFR AF: 0.935

Gnomad4 AMR AF: 0.727

Gnomad4 ASJ AF: 0.672

Gnomad4 EAS AF: 0.853

Gnomad4 SAS AF: 0.570

Gnomad4 FIN AF: 0.701

Gnomad4 NFE AF: 0.679

Gnomad4 OTH AF: 0.735

Alfa AF: 0.681 Hom.: 45627

Bravo AF: 0.770

Asia WGS AF: 0.714 AC: 2480 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.35
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1217394; hg19: chr1-114433659; COSMIC: COSV56726378;