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. The variant received -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
• Publications: 5 publications found

Genes affected

ENSG00000254363 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000607850.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC101929719	NR_130738.1		n.203+713G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000254363	ENST00000607850.1	TSL:5	n.3573G>A		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000254363	ENST00000523154.6	TSL:4	n.203+713G>A		intron	N/A
	ENSG00000254363	ENST00000719408.1		n.130+810G>A		intron	N/A

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

African (AFR) AF: 0.00 AC: 0 AN: 6

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.00 AC: 0 AN: 6

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.148 AC: 21 AN: 142

Other (OTH) AF: 0.00 AC: 0 AN: 8

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

African (AFR) AF: 0.0216 AC: 896 AN: 41496

American (AMR) AF: 0.0560 AC: 855 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0288 AC: 100 AN: 3468

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5184

South Asian (SAS) AF: 0.0145 AC: 70 AN: 4818

European-Finnish (FIN) AF: 0.127 AC: 1338 AN: 10568

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8580 AN: 67978

Other (OTH) AF: 0.0621 AC: 131 AN: 2108

Alfa AF: 0.107 Hom.: 640

Bravo AF: 0.0705

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.0
DANN	Benign	0.62
PhyloP100		0.26
Mutation Taster		=99/1	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs4913069; hg19: chr5-139545110;