7-106731773-C-G

Variant summary

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

The ENST00000490856.5(ENSG00000243797):n.108+569G>C 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 0.417 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: ENST00000490856.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000490856.5	n.108+569G>C		intron_variant, non_coding_transcript_variant		4
	ENST00000592441.1	n.172+28793G>C		intron_variant, non_coding_transcript_variant		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;