rs4913069

Variant names:

• chr5-140165525-G-A
• rs4913069
• ENST00000607850.1:n.3573G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-140165525-G-A
• chr5-140165525-G-T

Variant summary

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

The ENST00000607850.1(ENSG00000254363):​n.3573G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0792 in 152,250 control chromosomes in the GnomAD database, including 668 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 0.079 (666 hom., cov: 31)
  • Exomes 𝑓: 0.13 (2 hom.)
• Consequence: ENSG00000254363 ENST00000607850.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257

Genes affected

ENSG00000254363 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929719	NR_130738.1	n.203+713G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254363	ENST00000607850.1	n.3573G>A		non_coding_transcript_exon_variant	Exon 1 of 3	5
ENSG00000254363	ENST00000523154.5	n.203+713G>A		intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes AF: 0.0792 AC: 12038 AN: 151964 Hom.: 666 Cov.: 31

Gnomad AFR AF: 0.0217

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.0562

Gnomad ASJ AF: 0.0288

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0143

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.0628

GnomAD4 exome AF: 0.125 AC: 21 AN: 168 Hom.: 2 Cov.: 0 AF XY: 0.123 AC XY: 16 AN XY: 130

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.148

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0791 AC: 12036 AN: 152082 Hom.: 666 Cov.: 31 AF XY: 0.0776 AC XY: 5767 AN XY: 74334

Gnomad4 AFR AF: 0.0216

Gnomad4 AMR AF: 0.0560

Gnomad4 ASJ AF: 0.0288

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0145

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.0621

Alfa AF: 0.107 Hom.: 453

Bravo AF: 0.0705

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.0
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4913069; hg19: chr5-139545110;