rs8064821

chr17-78361310-C-A

Variant summary

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

The NR_110847.1(SOCS3-DT):n.326+537C>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 0.168 in 152,066 control chromosomes in the GnomAD database, including 2,516 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 0.17 (2516 hom., cov: 32)
• Consequence: SOCS3-DT NR_110847.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SOCS3-DT	NR_110847.1	n.326+537C>A		intron_variant, non_coding_transcript_variant
SOCS3-DT	NR_110845.1	n.327-456C>A		intron_variant, non_coding_transcript_variant
SOCS3-DT	NR_110846.1	n.59+250C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SOCS3-DT	ENST00000592569.1	n.321+537C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25526 AN: 151946 Hom.: 2511 Cov.: 32

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.168 AC: 25559 AN: 152066 Hom.: 2516 Cov.: 32 AF XY: 0.169 AC XY: 12597 AN XY: 74330

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.171

Alfa AF: 0.146 Hom.: 546

Bravo AF: 0.170

Asia WGS AF: 0.211 AC: 733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	0.94
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8064821; hg19: chr17-76357391;