ENST00000819164.1:n.67-642C>T

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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306507	ENST00000819164.1	n.67-642C>T		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs5979785; hg19: chrX-12971524;