chr5-75832358-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC391798		n.75832358G>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000251419	ENST00000505953.1	n.407C>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

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 v4.3

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

Other links and lift over

dbSNP: rs10515209; hg19: chr5-75128183;