4-119393726-A-G

Variant names:

• chr4-119393726-A-G
• rs4309825
• ENST00000505994.1:n.1610T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000720596.1(ENSG00000294020):​n.1039A>G 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: ENSG00000294020 ENST00000720596.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.79
• Publications: 7 publications found

Genes affected

ENSG00000249244 (HGNC:23263):

ENSG00000294020 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000720596.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000249244	ENST00000505994.1	TSL:6	n.1610T>C		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000294020	ENST00000720596.1		n.1039A>G		non_coding_transcript_exon	Exon 7 of 7
	ENSG00000294020	ENST00000720597.1		n.998A>G		non_coding_transcript_exon	Exon 6 of 6

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

African (AFR) AF: 0.256 AC: 6779 AN: 26522

American (AMR) AF: 0.289 AC: 12795 AN: 44290

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 4671 AN: 23930

East Asian (EAS) AF: 0.336 AC: 12746 AN: 37918

South Asian (SAS) AF: 0.164 AC: 13001 AN: 79376

European-Finnish (FIN) AF: 0.253 AC: 13506 AN: 53294

Middle Eastern (MID) AF: 0.171 AC: 876 AN: 5112

European-Non Finnish (NFE) AF: 0.265 AC: 204318 AN: 770392

Other (OTH) AF: 0.254 AC: 12229 AN: 48196

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

African (AFR) AF: 0.273 AC: 11321 AN: 41518

American (AMR) AF: 0.269 AC: 4108 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 657 AN: 3470

East Asian (EAS) AF: 0.378 AC: 1956 AN: 5172

South Asian (SAS) AF: 0.176 AC: 847 AN: 4824

European-Finnish (FIN) AF: 0.255 AC: 2703 AN: 10586

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19930 AN: 68000

Other (OTH) AF: 0.285 AC: 602 AN: 2114

Alfa AF: 0.170 Hom.: 448

Bravo AF: 0.287

Asia WGS AF: 0.253 AC: 879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	15
DANN	Benign	0.87
PhyloP100		4.8

Splicing

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

Other links and lift over

dbSNP: rs4309825; hg19: chr4-120314881;