rs342296

chr7-106732457-G-A

Variant summary

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

The ENST00000592441.1(ENSG00000243797):n.172+28109C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 151,996 control chromosomes in the GnomAD database, including 13,244 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 (13239 hom., cov: 31)
  • Exomes 𝑓: 0.50 (5 hom.)
• Consequence: ENST00000592441.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000592441.1	n.172+28109C>T		intron_variant, non_coding_transcript_variant		2
	ENST00000490856.5			upstream_gene_variant		4

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62533 AN: 151852 Hom.: 13221 Cov.: 31

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.405

GnomAD4 exome AF: 0.500 AC: 13 AN: 26 Hom.: 5 Cov.: 0 AF XY: 0.500 AC XY: 11 AN XY: 22

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.333

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.412 AC: 62588 AN: 151970 Hom.: 13239 Cov.: 31 AF XY: 0.410 AC XY: 30434 AN XY: 74300

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.401

Alfa AF: 0.439 Hom.: 9816

Bravo AF: 0.401

Asia WGS AF: 0.324 AC: 1129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.3
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs342296; hg19: chr7-106372903;