rs11868378

Positions:

• chr17-78361793-G-A
• chr17-78361793-G-C

Variant summary

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

The NR_110847.1(SOCS3-DT):​n.327-880G>A 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 0.736 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 NR_110847.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.615

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SOCS3-DT	NR_110847.1	n.327-880G>A		intron_variant, non_coding_transcript_variant
SOCS3-DT	NR_110845.1	n.354G>A		non_coding_transcript_exon_variant	2/4
SOCS3-DT	NR_110846.1	n.59+733G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SOCS3-DT	ENST00000592569.1	n.322-880G>A		intron_variant, non_coding_transcript_variant		3
SOCS3-DT	ENST00000687996.2	n.399-880G>A		intron_variant, non_coding_transcript_variant
SOCS3-DT	ENST00000689065.1	n.355-880G>A		intron_variant, non_coding_transcript_variant
SOCS3-DT	ENST00000691100.1	n.600+733G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.662

Gnomad4 AMR AF: 0.771

Gnomad4 ASJ AF: 0.756

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.760

Gnomad4 FIN AF: 0.749

Gnomad4 NFE AF: 0.791

Gnomad4 OTH AF: 0.720

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11868378; hg19: chr17-76357874;