rs536036

Variant names:

• chr3-57292855-G-A
• rs536036
• XR_007095923.1:n.65G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-57292855-G-A
• chr3-57292855-G-C
• chr3-57292855-G-T

Variant summary

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

The XR_007095923.1(LOC124909384):​n.65G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.668 in 152,042 control chromosomes in the GnomAD database, including 34,226 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 (34226 hom., cov: 32)
• Consequence: LOC124909384 XR_007095923.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.718
• Publications: 5 publications found

Genes affected

LOC124909384 (HGNC:):

ASB14 (HGNC:19766): (ankyrin repeat and SOCS box containing 14) The protein encoded by this gene is a member of the ankyrin repeat and SOCS box-containing (ASB) family of proteins. They contain ankyrin repeat sequence and a SOCS box domain. The SOCS box serves to couple suppressor of cytokine signalling (SOCS) proteins and their binding partners with the elongin B and C complex, possibly targeting them for degradation. Alternative splicing results in multiple transcript variants encoding different isoforms.[provided by RefSeq, Dec 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000487349.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASB14	NM_001142733.3	MANE Select	c.-294C>T		upstream_gene	N/A	NP_001136205.2	A6NK59-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASB14	ENST00000487349.6	TSL:1 MANE Select	c.-294C>T		upstream_gene	N/A	ENSP00000419199.1	A6NK59-3
	ENSG00000286952	ENST00000656348.1		n.-228G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.668 AC: 101476 AN: 151924 Hom.: 34178 Cov.: 32

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.668 AC: 101579 AN: 152042 Hom.: 34226 Cov.: 32 AF XY: 0.673 AC XY: 49992 AN XY: 74294

African (AFR) AF: 0.705 AC: 29256 AN: 41480

American (AMR) AF: 0.745 AC: 11373 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 1960 AN: 3468

East Asian (EAS) AF: 0.924 AC: 4789 AN: 5184

South Asian (SAS) AF: 0.648 AC: 3118 AN: 4812

European-Finnish (FIN) AF: 0.696 AC: 7335 AN: 10542

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.613 AC: 41628 AN: 67964

Other (OTH) AF: 0.659 AC: 1391 AN: 2112

Alfa AF: 0.641 Hom.: 4682

Bravo AF: 0.675

Asia WGS AF: 0.778 AC: 2703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.8
DANN	Benign	0.40
PhyloP100		-0.72
PromoterAI		-0.0084	Neutral

Splicing

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

Other links and lift over

dbSNP: rs536036; hg19: chr3-57326883;