rs4309825

Positions:

• chr4-119393726-A-G

Variant summary

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

The ENST00000505994.1(ENSG00000249244):​n.1610T>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.261 in 1,241,204 control chromosomes in the GnomAD database, including 43,096 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 0.28 (6020 hom., cov: 32)
  • Exomes 𝑓: 0.26 (37076 hom.)
• Consequence: ENST00000505994.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.79

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986193	XR_001741431.2	n.3189A>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000505994.1	n.1610T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42416 AN: 152058 Hom.: 6018 Cov.: 32

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.286

GnomAD4 exome AF: 0.258 AC: 280921 AN: 1089030 Hom.: 37076 Cov.: 16 AF XY: 0.255 AC XY: 142642 AN XY: 559706

Gnomad4 AFR exome AF: 0.256

Gnomad4 AMR exome AF: 0.289

Gnomad4 ASJ exome AF: 0.195

Gnomad4 EAS exome AF: 0.336

Gnomad4 SAS exome AF: 0.164

Gnomad4 FIN exome AF: 0.253

Gnomad4 NFE exome AF: 0.265

Gnomad4 OTH exome AF: 0.254

GnomAD4 genome AF: 0.279 AC: 42443 AN: 152174 Hom.: 6020 Cov.: 32 AF XY: 0.276 AC XY: 20553 AN XY: 74398

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.378

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.285

Alfa AF: 0.166 Hom.: 423

Bravo AF: 0.287

Asia WGS AF: 0.253 AC: 879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	15
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4309825; hg19: chr4-120314881;