chr17-78361793-G-A

Variant names:

• chr17-78361793-G-A
• rs11868378
• ENST00000717046.1:n.436G>A

Variant summary

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

The ENST00000717046.1(SOCS3-DT):​n.436G>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 0.736 in 152,064 control chromosomes in the GnomAD database, including 41,626 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 0.74 (41626 hom., cov: 31)
• Consequence: SOCS3-DT ENST00000717046.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.615
• Publications: 7 publications found

Genes affected

SOCS3-DT (HGNC:52799): (SOCS3 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000717046.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOCS3-DT	NR_110845.1		n.354G>A		non_coding_transcript_exon	Exon 2 of 4
	SOCS3-DT	NR_110846.1		n.59+733G>A		intron	N/A
	SOCS3-DT	NR_110847.1		n.327-880G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOCS3-DT	ENST00000717046.1		n.436G>A		non_coding_transcript_exon	Exon 2 of 4
	SOCS3-DT	ENST00000794149.1		n.363G>A		non_coding_transcript_exon	Exon 2 of 4
	SOCS3-DT	ENST00000794150.1		n.355G>A		non_coding_transcript_exon	Exon 2 of 6

Frequencies

GnomAD3 genomes AF: 0.736 AC: 111803 AN: 151946 Hom.: 41600 Cov.: 31

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.756

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.762

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.718

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

GnomAD4 genome AF: 0.736 AC: 111875 AN: 152064 Hom.: 41626 Cov.: 31 AF XY: 0.733 AC XY: 54469 AN XY: 74310

African (AFR) AF: 0.662 AC: 27451 AN: 41468

American (AMR) AF: 0.771 AC: 11788 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.756 AC: 2625 AN: 3470

East Asian (EAS) AF: 0.424 AC: 2189 AN: 5164

South Asian (SAS) AF: 0.760 AC: 3665 AN: 4820

European-Finnish (FIN) AF: 0.749 AC: 7907 AN: 10560

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.791 AC: 53794 AN: 67980

Other (OTH) AF: 0.720 AC: 1523 AN: 2114

Alfa AF: 0.668 Hom.: 1959

Bravo AF: 0.731

Asia WGS AF: 0.610 AC: 2124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.83
DANN	Benign	0.23
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs11868378; hg19: chr17-76357874;