7-106557366-T-C

Variant names:

• chr7-106557366-T-C
• rs7792872
• ENST00000485282.5:n.311+53031A>G

Variant summary

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

The ENST00000592441.1(ENSG00000243797):​n.239+53031A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.791 in 152,070 control chromosomes in the GnomAD database, including 49,205 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 0.79 (49205 hom., cov: 31)
• Consequence: ENSG00000243797 ENST00000592441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.55

Genes affected

ENSG00000243797 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.945 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	ENST00000485282.5	n.311+53031A>G		intron_variant	Intron 3 of 4	3
ENSG00000243797	ENST00000490856.5	n.176-36547A>G		intron_variant	Intron 2 of 4	4
ENSG00000243797	ENST00000592441.1	n.239+53031A>G		intron_variant	Intron 3 of 4	2

Frequencies

GnomAD3 genomes AF: 0.791 AC: 120182 AN: 151952 Hom.: 49145 Cov.: 31

Gnomad AFR AF: 0.952

Gnomad AMI AF: 0.856

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.791 AC: 120301 AN: 152070 Hom.: 49205 Cov.: 31 AF XY: 0.781 AC XY: 58037 AN XY: 74312

Gnomad4 AFR AF: 0.952

Gnomad4 AMR AF: 0.783

Gnomad4 ASJ AF: 0.773

Gnomad4 EAS AF: 0.251

Gnomad4 SAS AF: 0.641

Gnomad4 FIN AF: 0.653

Gnomad4 NFE AF: 0.767

Gnomad4 OTH AF: 0.805

Alfa AF: 0.752 Hom.: 16196

Bravo AF: 0.810

Asia WGS AF: 0.498 AC: 1734 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.018
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7792872; hg19: chr7-106197812;