rs4243628

Positions:

• chr14-64386954-G-T

Variant summary

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

The ENST00000641479.1(ENSG00000293482):​n.570+463C>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 0.375 in 152,154 control chromosomes in the GnomAD database, including 13,166 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 0.38 (13158 hom., cov: 33)
  • Exomes 𝑓: 0.56 (8 hom.)
• Consequence: ENST00000641479.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243

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 (NFE) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000641479.1	n.570+463C>A		intron_variant, non_coding_transcript_variant
	ENST00000641725.1	n.100C>A		non_coding_transcript_exon_variant	1/6
	ENST00000689962.1	n.986C>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.375 AC: 57050 AN: 151986 Hom.: 13158 Cov.: 33

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.442

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.395

GnomAD4 exome AF: 0.560 AC: 28 AN: 50 Hom.: 8 Cov.: 0 AF XY: 0.595 AC XY: 25 AN XY: 42

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.625

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.375 AC: 57059 AN: 152104 Hom.: 13158 Cov.: 33 AF XY: 0.383 AC XY: 28449 AN XY: 74356

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.467

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.567

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.397

Alfa AF: 0.435 Hom.: 2000

Bravo AF: 0.355

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.4
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4243628; hg19: chr14-64853672;