17-78369710-T-C

Variant names:

• chr17-78369710-T-C
• rs4969172
• ENST00000794162.1:n.56T>C

Variant summary

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

The ENST00000794162.1(SOCS3-DT):​n.56T>C 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 0.528 in 152,040 control chromosomes in the GnomAD database, including 23,282 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 0.53 (23282 hom., cov: 32)
• Consequence: SOCS3-DT ENST00000794162.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000794162.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOCS3-DT	NR_110847.1		n.645+817T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOCS3-DT	ENST00000794162.1		n.56T>C		non_coding_transcript_exon	Exon 1 of 2
	SOCS3-DT	ENST00000794163.1		n.32T>C		non_coding_transcript_exon	Exon 1 of 2
	SOCS3-DT	ENST00000794168.1		n.231T>C		non_coding_transcript_exon	Exon 3 of 5

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80305 AN: 151922 Hom.: 23289 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.528 AC: 80313 AN: 152040 Hom.: 23282 Cov.: 32 AF XY: 0.529 AC XY: 39273 AN XY: 74306

African (AFR) AF: 0.322 AC: 13370 AN: 41476

American (AMR) AF: 0.577 AC: 8815 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1855 AN: 3466

East Asian (EAS) AF: 0.106 AC: 550 AN: 5172

South Asian (SAS) AF: 0.529 AC: 2549 AN: 4814

European-Finnish (FIN) AF: 0.670 AC: 7080 AN: 10560

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.651 AC: 44209 AN: 67960

Other (OTH) AF: 0.521 AC: 1100 AN: 2112

Alfa AF: 0.584 Hom.: 55457

Bravo AF: 0.507

Asia WGS AF: 0.355 AC: 1234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.47
PhyloP100		-1.9

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4969172;

hg19: chr17-76365791;