rs342294

Variant names:

• chr7-106732176-T-C
• rs342294
• ENST00000490856.5:n.108+166A>G

Variant summary

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

The ENST00000490856.5(ENSG00000243797):​n.108+166A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 151,812 control chromosomes in the GnomAD database, including 13,391 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 0.41 (13391 hom., cov: 29)
• Consequence: ENSG00000243797 ENST00000490856.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 3 publications found

Genes affected

ENSG00000243797 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000490856.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000243797	ENST00000490856.5	TSL:4	n.108+166A>G		intron	N/A
	ENSG00000243797	ENST00000592441.1	TSL:2	n.172+28390A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.415 AC: 62932 AN: 151692 Hom.: 13373 Cov.: 29

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.415 AC: 62989 AN: 151812 Hom.: 13391 Cov.: 29 AF XY: 0.412 AC XY: 30590 AN XY: 74178

African (AFR) AF: 0.380 AC: 15738 AN: 41394

American (AMR) AF: 0.367 AC: 5598 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1721 AN: 3468

East Asian (EAS) AF: 0.235 AC: 1209 AN: 5146

South Asian (SAS) AF: 0.359 AC: 1726 AN: 4804

European-Finnish (FIN) AF: 0.472 AC: 4973 AN: 10534

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.453 AC: 30797 AN: 67918

Other (OTH) AF: 0.405 AC: 853 AN: 2106

Alfa AF: 0.425 Hom.: 8310

Bravo AF: 0.405

Asia WGS AF: 0.327 AC: 1138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.36
DANN	Benign	0.45
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs342294; hg19: chr7-106372622;