1-170513160-T-C

Variant names:

• chr1-170513160-T-C
• rs1928716
• ENST00000416416.1:n.113+4434A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000416416.1(GORAB-AS1):​n.113+4434A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.67 in 152,104 control chromosomes in the GnomAD database, including 34,663 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 0.67 (34663 hom., cov: 32)
• Consequence: GORAB-AS1 ENST00000416416.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.975
• Publications: 4 publications found

Genes affected

GORAB-AS1 (HGNC:54051): (GORAB antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GORAB-AS1	NR_125958.1	n.162+19288A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GORAB-AS1	ENST00000416416.1	n.113+4434A>G		intron_variant	Intron 1 of 1	5
GORAB-AS1	ENST00000421020.1	n.296-2740A>G		intron_variant	Intron 3 of 3	3
GORAB-AS1	ENST00000456083.6	n.310+4434A>G		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.670 AC: 101846 AN: 151986 Hom.: 34611 Cov.: 32

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.830

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.670 AC: 101955 AN: 152104 Hom.: 34663 Cov.: 32 AF XY: 0.676 AC XY: 50276 AN XY: 74348

African (AFR) AF: 0.697 AC: 28929 AN: 41486

American (AMR) AF: 0.708 AC: 10823 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2215 AN: 3468

East Asian (EAS) AF: 0.993 AC: 5143 AN: 5180

South Asian (SAS) AF: 0.831 AC: 4008 AN: 4826

European-Finnish (FIN) AF: 0.638 AC: 6730 AN: 10550

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.620 AC: 42122 AN: 67992

Other (OTH) AF: 0.664 AC: 1403 AN: 2112

Alfa AF: 0.645 Hom.: 16948

Bravo AF: 0.673

Asia WGS AF: 0.908 AC: 3157 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.1
DANN	Benign	0.72
PhyloP100		0.97

Splicing

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

Other links and lift over

dbSNP: rs1928716; hg19: chr1-170482301;