rs2340419

Variant names:

• chrX-128383343-C-T
• rs2340419
• ENST00000449485.2:n.412-46971G>A

Variant summary

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

The ENST00000657074.1(ENSG00000225689):​n.3400-46971G>A 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 0.99 (38407 hom., 33137 hem., cov: 24)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000225689 ENST00000657074.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 1 publications found

Genes affected

ENSG00000225689 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000657074.1. 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
	ENSG00000225689	ENST00000449485.2	TSL:5	n.412-46971G>A		intron	N/A
	ENSG00000225689	ENST00000657074.1		n.3400-46971G>A		intron	N/A
	ENSG00000225689	ENST00000660383.1		n.927-46971G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.994 AC: 110404 AN: 111121 Hom.: 38411 Cov.: 24

Gnomad AFR AF: 0.978

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.996

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 1.00

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.995

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: 0.994 AC: 110460 AN: 111176 Hom.: 38407 Cov.: 24 AF XY: 0.994 AC XY: 33137 AN XY: 33336

African (AFR) AF: 0.978 AC: 29840 AN: 30509

American (AMR) AF: 0.996 AC: 10396 AN: 10433

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2643 AN: 2643

East Asian (EAS) AF: 1.00 AC: 3532 AN: 3532

South Asian (SAS) AF: 1.00 AC: 2648 AN: 2648

European-Finnish (FIN) AF: 1.00 AC: 5830 AN: 5830

Middle Eastern (MID) AF: 1.00 AC: 216 AN: 216

European-Non Finnish (NFE) AF: 1.00 AC: 53157 AN: 53160

Other (OTH) AF: 0.995 AC: 1516 AN: 1523

Alfa AF: 0.996 Hom.: 11249

Bravo AF: 0.992

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.85
DANN	Benign	0.55
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: rs2340419;

hg19: chrX-127517321;