1-113887734-C-T

Position:

• chr1-113887734-C-T

Variant summary

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

The NR_125965.1(AP4B1-AS1):​n.415-10134C>T 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 0.759 in 152,178 control chromosomes in the GnomAD database, including 44,823 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 (44823 hom., cov: 32)
• Consequence: AP4B1-AS1 NR_125965.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662

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=-0.88).
• 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.415-10134C>T		intron_variant, non_coding_transcript_variant
AP4B1-AS1	NR_037864.1	n.247-10134C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AP4B1-AS1	ENST00000419536.1	n.247-10134C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.758 AC: 115321 AN: 152060 Hom.: 44770 Cov.: 32

Gnomad AFR AF: 0.935

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.759 AC: 115431 AN: 152178 Hom.: 44823 Cov.: 32 AF XY: 0.757 AC XY: 56319 AN XY: 74400

Gnomad4 AFR AF: 0.935

Gnomad4 AMR AF: 0.728

Gnomad4 ASJ AF: 0.677

Gnomad4 EAS AF: 0.854

Gnomad4 SAS AF: 0.570

Gnomad4 FIN AF: 0.701

Gnomad4 NFE AF: 0.679

Gnomad4 OTH AF: 0.736

Alfa AF: 0.689 Hom.: 61832

Bravo AF: 0.770

Asia WGS AF: 0.713 AC: 2478 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.74
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1539438; hg19: chr1-114430356;