5-75832358-G-C

Variant names:

• chr5-75832358-G-C
• rs10515209
• ENST00000505953.1:n.407C>G

Variant summary

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

The ENST00000505953.1(ENSG00000251419):​n.407C>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0371 in 1,269,374 control chromosomes in the GnomAD database, including 2,457 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 0.068 (744 hom., cov: 32)
  • Exomes 𝑓: 0.033 (1713 hom.)
• Consequence: ENSG00000251419 ENST00000505953.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.41
• Publications: 1 publications found

Genes affected

ENSG00000251419 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000505953.1. 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
	ENSG00000251419	ENST00000505953.1	TSL:6	n.407C>G		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0676 AC: 10277 AN: 152012 Hom.: 743 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0383

Gnomad ASJ AF: 0.0683

Gnomad EAS AF: 0.0736

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0113

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0158

Gnomad OTH AF: 0.0612

GnomAD4 exome AF: 0.0329 AC: 36754 AN: 1117244 Hom.: 1713 Cov.: 17 AF XY: 0.0357 AC XY: 20116 AN XY: 563174

African (AFR) AF: 0.184 AC: 4916 AN: 26768

American (AMR) AF: 0.0231 AC: 813 AN: 35226

Ashkenazi Jewish (ASJ) AF: 0.0768 AC: 1790 AN: 23320

East Asian (EAS) AF: 0.103 AC: 3495 AN: 34038

South Asian (SAS) AF: 0.118 AC: 8620 AN: 73322

European-Finnish (FIN) AF: 0.00931 AC: 453 AN: 48654

Middle Eastern (MID) AF: 0.0973 AC: 497 AN: 5106

European-Non Finnish (NFE) AF: 0.0169 AC: 13926 AN: 822576

Other (OTH) AF: 0.0465 AC: 2244 AN: 48234

GnomAD4 genome AF: 0.0677 AC: 10303 AN: 152130 Hom.: 744 Cov.: 32 AF XY: 0.0667 AC XY: 4960 AN XY: 74378

African (AFR) AF: 0.173 AC: 7187 AN: 41476

American (AMR) AF: 0.0382 AC: 584 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0683 AC: 237 AN: 3472

East Asian (EAS) AF: 0.0742 AC: 383 AN: 5162

South Asian (SAS) AF: 0.115 AC: 555 AN: 4810

European-Finnish (FIN) AF: 0.0113 AC: 120 AN: 10604

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0158 AC: 1076 AN: 68008

Other (OTH) AF: 0.0639 AC: 135 AN: 2112

Alfa AF: 0.0121 Hom.: 10

Bravo AF: 0.0727

Asia WGS AF: 0.109 AC: 382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	3.1
DANN	Benign	0.67
PhyloP100		5.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10515209;

hg19: chr5-75128183;