rs342292

Variant names:

• chr7-106730198-C-G
• rs342292
• ENST00000490856.5:n.108+2144G>C

Your query was ambiguous. Multiple possible variants found:

• chr7-106730198-C-G
• chr7-106730198-C-T

Variant summary

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

The ENST00000490856.5(ENSG00000243797):​n.108+2144G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 151,830 control chromosomes in the GnomAD database, including 12,520 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 0.40 (12520 hom., cov: 31)
• Consequence: ENSG00000243797 ENST00000490856.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.849
• Publications: 4 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 = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000243797	ENST00000490856.5	n.108+2144G>C		intron_variant	Intron 1 of 4	4
ENSG00000243797	ENST00000592441.1	n.172+30368G>C		intron_variant	Intron 2 of 4	2

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60483 AN: 151714 Hom.: 12510 Cov.: 31

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.399 AC: 60523 AN: 151830 Hom.: 12520 Cov.: 31 AF XY: 0.397 AC XY: 29480 AN XY: 74168

African (AFR) AF: 0.321 AC: 13277 AN: 41382

American (AMR) AF: 0.363 AC: 5520 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1724 AN: 3468

East Asian (EAS) AF: 0.238 AC: 1231 AN: 5166

South Asian (SAS) AF: 0.375 AC: 1803 AN: 4814

European-Finnish (FIN) AF: 0.476 AC: 5010 AN: 10532

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

European-Non Finnish (NFE) AF: 0.453 AC: 30752 AN: 67932

Other (OTH) AF: 0.392 AC: 826 AN: 2108

Alfa AF: 0.422 Hom.: 1650

Bravo AF: 0.386

Asia WGS AF: 0.336 AC: 1168 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.8
DANN	Benign	0.71
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs342292; hg19: chr7-106370644;