rs1217411

Positions:

• chr1-113813503-A-G

Variant summary

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

The NR_125965.1(AP4B1-AS1):​n.214+678A>G 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 0.561 in 151,754 control chromosomes in the GnomAD database, including 24,568 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 0.56 (24568 hom., cov: 30)
• Consequence: AP4B1-AS1 NR_125965.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.672

Genes affected

(HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AP4B1-AS1	NR_125965.1	n.214+678A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000664434.1	n.218+678A>G		intron_variant, non_coding_transcript_variant
	ENST00000418238.2	n.179+678A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000429398.5	n.235-884A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000702317.1			downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.560 AC: 84987 AN: 151636 Hom.: 24542 Cov.: 30

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.561 AC: 85062 AN: 151754 Hom.: 24568 Cov.: 30 AF XY: 0.555 AC XY: 41177 AN XY: 74148

Gnomad4 AFR AF: 0.635

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.609

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.651

Gnomad4 FIN AF: 0.504

Gnomad4 NFE AF: 0.570

Gnomad4 OTH AF: 0.543

Alfa AF: 0.570 Hom.: 3078

Bravo AF: 0.551

Asia WGS AF: 0.437 AC: 1520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1217411; hg19: chr1-114356125;