rs4899337

Positions:

• chr14-70204466-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_135825.1(LOC646548):​n.278+11945C>A variant causes a intron, non coding transcript 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: LOC646548 NR_135825.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.113

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC646548	NR_135825.1	n.278+11945C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000555480.5	n.263+11945C>A		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.423

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.494

Gnomad4 EAS AF: 0.595

Gnomad4 SAS AF: 0.393

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.400

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4899337; hg19: chr14-70671183;