17-78364457-A-G

Variant names:

• chr17-78364457-A-G
• rs4969170
• ENST00000794181.1:n.998A>G

Variant summary

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

The ENST00000794181.1(SOCS3-DT):​n.998A>G 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 0.538 in 151,994 control chromosomes in the GnomAD database, including 23,938 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 0.54 (23935 hom., cov: 32)
  • Exomes 𝑓: 0.56 (3 hom.)
• Consequence: SOCS3-DT ENST00000794181.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19
• Publications: 55 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000794181.1. 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.462-40A>G		intron	N/A
	SOCS3-DT	NR_110846.1		n.139-40A>G		intron	N/A
	SOCS3-DT	NR_110847.1		n.405+1706A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOCS3-DT	ENST00000794181.1		n.998A>G		non_coding_transcript_exon	Exon 4 of 4
	SOCS3-DT	ENST00000587575.1	TSL:3	n.82-40A>G		intron	N/A
	SOCS3-DT	ENST00000592569.1	TSL:3	n.400+1706A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81683 AN: 151860 Hom.: 23940 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.710

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.0985

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.529

GnomAD4 exome AF: 0.563 AC: 9 AN: 16 Hom.: 3 Cov.: 0 AF XY: 0.571 AC XY: 8 AN XY: 14

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 6 AN: 12

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.538 AC: 81697 AN: 151978 Hom.: 23935 Cov.: 32 AF XY: 0.538 AC XY: 39910 AN XY: 74246

African (AFR) AF: 0.342 AC: 14172 AN: 41452

American (AMR) AF: 0.582 AC: 8885 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1937 AN: 3472

East Asian (EAS) AF: 0.0985 AC: 510 AN: 5178

South Asian (SAS) AF: 0.536 AC: 2583 AN: 4822

European-Finnish (FIN) AF: 0.668 AC: 7035 AN: 10534

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.658 AC: 44686 AN: 67944

Other (OTH) AF: 0.524 AC: 1104 AN: 2106

Alfa AF: 0.607 Hom.: 100120

Bravo AF: 0.516

Asia WGS AF: 0.353 AC: 1230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.042
DANN	Benign	0.59
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs4969170; hg19: chr17-76360538;