1-113872746-G-C

Position:

• chr1-113872746-G-C

Variant summary

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

The NR_125965.1(AP4B1-AS1):​n.415-25122G>C 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 0.813 in 152,128 control chromosomes in the GnomAD database, including 51,265 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).

• Frequency: Genomes: 𝑓 0.81 (51265 hom., cov: 32)
• Consequence: AP4B1-AS1 NR_125965.1 intron, non_coding_transcript
• Clinical Significance: risk factor no assertion criteria provided O:1
• Conservation: PhyloP100: -0.196

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AP4B1-AS1	NR_125965.1	n.415-25122G>C		intron_variant, non_coding_transcript_variant
AP4B1-AS1	NR_037864.1	n.246+14730G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AP4B1-AS1	ENST00000419536.1	n.246+14730G>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.812 AC: 123506 AN: 152010 Hom.: 51201 Cov.: 32

Gnomad AFR AF: 0.958

Gnomad AMI AF: 0.877

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.801

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.789

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

GnomAD4 genome AF: 0.813 AC: 123632 AN: 152128 Hom.: 51265 Cov.: 32 AF XY: 0.806 AC XY: 59937 AN XY: 74338

Gnomad4 AFR AF: 0.958

Gnomad4 AMR AF: 0.739

Gnomad4 ASJ AF: 0.801

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.814

Gnomad4 FIN AF: 0.693

Gnomad4 NFE AF: 0.791

Gnomad4 OTH AF: 0.789

Alfa AF: 0.797 Hom.: 5716

Bravo AF: 0.813

Asia WGS AF: 0.677 AC: 2356 AN: 3478

ClinVar

Significance: risk factor

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Diabetes mellitus, insulin-dependent, susceptibility to Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Mar 15, 2006

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.8
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2488457; hg19: chr1-114415368;