rs5979785

Variant names:

• chrX-12953405-C-T
• rs5979785
• ENST00000819164.1:n.67-642C>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000819164.1(ENSG00000306507):​n.67-642C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.72 (21018 hom., 23335 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000306507 ENST00000819164.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.732
• Publications: 22 publications found

Genes affected

ENSG00000306507 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000819164.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306507	ENST00000819164.1		n.67-642C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.720 AC: 79796 AN: 110759 Hom.: 21019 Cov.: 23

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.787

Gnomad MID AF: 0.641

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.703

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.720 AC: 79825 AN: 110812 Hom.: 21018 Cov.: 23 AF XY: 0.706 AC XY: 23335 AN XY: 33042

African (AFR) AF: 0.798 AC: 24275 AN: 30413

American (AMR) AF: 0.621 AC: 6519 AN: 10495

Ashkenazi Jewish (ASJ) AF: 0.748 AC: 1971 AN: 2634

East Asian (EAS) AF: 0.201 AC: 709 AN: 3530

South Asian (SAS) AF: 0.466 AC: 1236 AN: 2652

European-Finnish (FIN) AF: 0.787 AC: 4593 AN: 5839

Middle Eastern (MID) AF: 0.620 AC: 132 AN: 213

European-Non Finnish (NFE) AF: 0.737 AC: 38969 AN: 52855

Other (OTH) AF: 0.696 AC: 1051 AN: 1509

Alfa AF: 0.716 Hom.: 91751

Bravo AF: 0.712

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.091
DANN	Benign	0.34
PhyloP100		-0.73

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: rs5979785;

hg19: chrX-12971524;