chr5-29996700-G-A

Variant names:

• chr5-29996700-G-A
• rs4342344
• ENST00000842753.1:n.40-1031C>T

Variant summary

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

The ENST00000842753.1(ENSG00000309642):​n.40-1031C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 151,708 control chromosomes in the GnomAD database, including 6,048 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 (6048 hom., cov: 32)
• Consequence: ENSG00000309642 ENST00000842753.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12
• Publications: 1 publications found

Genes affected

ENSG00000309642 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000842753.1. 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
	ENSG00000309642	ENST00000842753.1		n.40-1031C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41685 AN: 151590 Hom.: 6041 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.00213

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.275 AC: 41721 AN: 151708 Hom.: 6048 Cov.: 32 AF XY: 0.273 AC XY: 20258 AN XY: 74134

African (AFR) AF: 0.275 AC: 11403 AN: 41438

American (AMR) AF: 0.230 AC: 3503 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 907 AN: 3466

East Asian (EAS) AF: 0.00213 AC: 11 AN: 5160

South Asian (SAS) AF: 0.183 AC: 885 AN: 4828

European-Finnish (FIN) AF: 0.350 AC: 3683 AN: 10516

Middle Eastern (MID) AF: 0.259 AC: 75 AN: 290

European-Non Finnish (NFE) AF: 0.301 AC: 20384 AN: 67774

Other (OTH) AF: 0.282 AC: 596 AN: 2112

Alfa AF: 0.276 Hom.: 1006

Bravo AF: 0.267

Asia WGS AF: 0.0880 AC: 304 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	11
DANN	Benign	0.58
PhyloP100		1.1

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: rs4342344;

hg19: chr5-29996807;