1-113891324-G-A

Position:

• chr1-113891324-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_125965.1(AP4B1-AS1):​n.415-6544G>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 0.408 in 151,954 control chromosomes in the GnomAD database, including 15,479 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 (15479 hom., cov: 32)
• Consequence: AP4B1-AS1 NR_125965.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AP4B1-AS1	NR_125965.1	n.415-6544G>A		intron_variant, non_coding_transcript_variant
AP4B1-AS1	NR_037864.1	n.247-6544G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AP4B1-AS1	ENST00000419536.1	n.247-6544G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61850 AN: 151836 Hom.: 15450 Cov.: 32

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.0760

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.408 AC: 61928 AN: 151954 Hom.: 15479 Cov.: 32 AF XY: 0.399 AC XY: 29638 AN XY: 74258

Gnomad4 AFR AF: 0.704

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.0762

Gnomad4 SAS AF: 0.301

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.375

Alfa AF: 0.370 Hom.: 1431

Bravo AF: 0.414

Asia WGS AF: 0.218 AC: 759 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	16
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1217393; hg19: chr1-114433946;