rs1352015

Positions:

• chrX-66624001-G-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_021783.5(EDA2R):​c.-10-7971C>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 0.70 (20537 hom., 23889 hem., cov: 24)
  • Failed GnomAD Quality Control
• Consequence: EDA2R NM_021783.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

Genes affected

EDA2R (HGNC:17756): (ectodysplasin A2 receptor) The protein encoded by this gene is a type III transmembrane protein of the TNFR (tumor necrosis factor receptor) superfamily, and contains cysteine-rich repeats and a single transmembrane domain. This protein binds to the EDA-A2 isoform of ectodysplasin, which plays an important role in maintenance of hair and teeth. Alternatively spliced transcript variants encodes distinct protein isoforms. [provided by RefSeq, Apr 2016]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EDA2R	NM_021783.5	c.-10-7971C>T		intron_variant		ENST00000374719.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EDA2R	ENST00000374719.8	c.-10-7971C>T		intron_variant		1	NM_021783.5	P1
EDA2R	ENST00000451436.6	c.-10-7971C>T		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.704 AC: 78298 AN: 111174 Hom.: 20543 Cov.: 24 AF XY: 0.715 AC XY: 23879 AN XY: 33378

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.869

Gnomad AMR AF: 0.851

Gnomad ASJ AF: 0.922

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.902

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.748

Gnomad NFE AF: 0.800

Gnomad OTH AF: 0.749

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: 0.704 AC: 78296 AN: 111224 Hom.: 20537 Cov.: 24 AF XY: 0.714 AC XY: 23889 AN XY: 33438

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.852

Gnomad4 ASJ AF: 0.922

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.902

Gnomad4 FIN AF: 0.763

Gnomad4 NFE AF: 0.800

Gnomad4 OTH AF: 0.752

Alfa AF: 0.796 Hom.: 79371

Bravo AF: 0.700

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.12
DANN	Benign	0.45

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1352015; hg19: chrX-65843843;