7-106731773-C-G

Variant names:

• chr7-106731773-C-G
• rs342293
• ENST00000490856.5:n.108+569G>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000592441.1(ENSG00000243797):​n.172+28793G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 151,632 control chromosomes in the GnomAD database, including 13,484 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 0.42 (13484 hom., cov: 30)
• Consequence: ENSG00000243797 ENST00000592441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260

Genes affected

ENSG00000243797 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.451 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+569G>C		intron_variant	Intron 1 of 4	4
ENSG00000243797	ENST00000592441.1	n.172+28793G>C		intron_variant	Intron 2 of 4	2

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63148 AN: 151514 Hom.: 13468 Cov.: 30

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.417 AC: 63202 AN: 151632 Hom.: 13484 Cov.: 30 AF XY: 0.415 AC XY: 30717 AN XY: 74060

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.476

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.409

Alfa AF: 0.437 Hom.: 7997

Bravo AF: 0.407

Asia WGS AF: 0.330 AC: 1149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.7
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs342293; hg19: chr7-106372219;