14-70204466-C-A

Variant names:

• chr14-70204466-C-A
• rs4899337
• ENST00000555480.6:n.264+11945C>A

Variant summary

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

The ENST00000555480.6(ENSG00000258422):​n.264+11945C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 152,122 control chromosomes in the GnomAD database, including 10,845 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 0.37 (10845 hom., cov: 32)
• Consequence: ENSG00000258422 ENST00000555480.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.113
• Publications: 1 publications found

Genes affected

ENSG00000258422 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000555480.6. 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
	LOC646548	NR_135825.1		n.278+11945C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258422	ENST00000555480.6	TSL:4	n.264+11945C>A		intron	N/A
	ENSG00000258422	ENST00000726841.1		n.263+11945C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56586 AN: 152004 Hom.: 10836 Cov.: 32

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.372 AC: 56619 AN: 152122 Hom.: 10845 Cov.: 32 AF XY: 0.371 AC XY: 27633 AN XY: 74384

African (AFR) AF: 0.423 AC: 17536 AN: 41468

American (AMR) AF: 0.379 AC: 5801 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1712 AN: 3468

East Asian (EAS) AF: 0.595 AC: 3080 AN: 5178

South Asian (SAS) AF: 0.393 AC: 1895 AN: 4826

European-Finnish (FIN) AF: 0.272 AC: 2882 AN: 10580

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.332 AC: 22564 AN: 67986

Other (OTH) AF: 0.400 AC: 847 AN: 2116

Alfa AF: 0.347 Hom.: 1199

Bravo AF: 0.381

Asia WGS AF: 0.480 AC: 1666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.9
DANN	Benign	0.52
PhyloP100		0.11

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: rs4899337;

hg19: chr14-70671183;