rs4342344

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374706	XR_925890.1	n.212-1031C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309642	ENST00000842753.1	n.40-1031C>T		intron_variant	Intron 1 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs4342344; hg19: chr5-29996807;