1-113893860-G-A

Position:

• chr1-113893860-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.415-4008G>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 0.322 in 152,054 control chromosomes in the GnomAD database, including 9,533 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 0.32 (9533 hom., cov: 33)
• Consequence: AP4B1-AS1 NR_125965.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116

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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AP4B1-AS1	NR_125965.1	n.415-4008G>A		intron_variant, non_coding_transcript_variant
AP4B1-AS1	NR_037864.1	n.247-4008G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AP4B1-AS1	ENST00000419536.1	n.247-4008G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48934 AN: 151936 Hom.: 9540 Cov.: 33

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.322 AC: 48938 AN: 152054 Hom.: 9533 Cov.: 33 AF XY: 0.330 AC XY: 24503 AN XY: 74334

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.777

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.360

Gnomad4 OTH AF: 0.344

Alfa AF: 0.353 Hom.: 11088

Bravo AF: 0.324

Asia WGS AF: 0.489 AC: 1700 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10776775; hg19: chr1-114436482;