rs12952093

Positions:

• chr17-78367559-A-C
• chr17-78367559-A-G
• chr17-78367559-A-T

Variant summary

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

The NR_110847.1(SOCS3-DT):​n.479+293A>C 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 0.68 in 152,176 control chromosomes in the GnomAD database, including 35,464 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 0.68 (35464 hom., cov: 34)
• Consequence: SOCS3-DT NR_110847.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

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=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SOCS3-DT	NR_110847.1	n.479+293A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SOCS3-DT	ENST00000592569.1	n.474+293A>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.680 AC: 103455 AN: 152058 Hom.: 35442 Cov.: 34

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.680 AC: 103523 AN: 152176 Hom.: 35464 Cov.: 34 AF XY: 0.679 AC XY: 50474 AN XY: 74390

Gnomad4 AFR AF: 0.629

Gnomad4 AMR AF: 0.706

Gnomad4 ASJ AF: 0.666

Gnomad4 EAS AF: 0.483

Gnomad4 SAS AF: 0.692

Gnomad4 FIN AF: 0.691

Gnomad4 NFE AF: 0.719

Gnomad4 OTH AF: 0.669

Alfa AF: 0.588 Hom.: 1722

Bravo AF: 0.678

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.34
DANN	Benign	0.13

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12952093; hg19: chr17-76363640;