chr5-29793723-G-C

Variant names:

• chr5-29793723-G-C
• rs10520950
• ENST00000741457.1:n.22G>C

Variant summary

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

The ENST00000741457.1(ENSG00000296733):​n.22G>C 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 0.0978 in 152,072 control chromosomes in the GnomAD database, including 2,105 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 0.098 (2105 hom., cov: 32)
• Consequence: ENSG00000296733 ENST00000741457.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.687
• Publications: 0 publications found

Genes affected

ENSG00000296733 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000741457.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296733	ENST00000741457.1		n.22G>C		non_coding_transcript_exon	Exon 1 of 4
	ENSG00000296733	ENST00000741458.1		n.15G>C		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000296749	ENST00000741537.1		n.217+2224C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0976 AC: 14832 AN: 151954 Hom.: 2094 Cov.: 32

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0331

Gnomad ASJ AF: 0.00720

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.0234

Gnomad FIN AF: 0.0219

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00400

Gnomad OTH AF: 0.0733

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0978 AC: 14873 AN: 152072 Hom.: 2105 Cov.: 32 AF XY: 0.0963 AC XY: 7158 AN XY: 74338

African (AFR) AF: 0.305 AC: 12641 AN: 41440

American (AMR) AF: 0.0330 AC: 504 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.00720 AC: 25 AN: 3470

East Asian (EAS) AF: 0.177 AC: 917 AN: 5174

South Asian (SAS) AF: 0.0234 AC: 113 AN: 4834

European-Finnish (FIN) AF: 0.0219 AC: 232 AN: 10608

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00400 AC: 272 AN: 67972

Other (OTH) AF: 0.0758 AC: 160 AN: 2110

Alfa AF: 0.0151 Hom.: 27

Bravo AF: 0.108

Asia WGS AF: 0.102 AC: 356 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.60
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs10520950; hg19: chr5-29793830;