chr7-106557366-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.945 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000592441.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000243797	ENST00000485282.5	TSL:3	n.311+53031A>G		intron	N/A
	ENSG00000243797	ENST00000490856.5	TSL:4	n.176-36547A>G		intron	N/A
	ENSG00000243797	ENST00000592441.1	TSL:2	n.239+53031A>G		intron	N/A

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

African (AFR) AF: 0.952 AC: 39535 AN: 41512

American (AMR) AF: 0.783 AC: 11968 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.773 AC: 2681 AN: 3468

East Asian (EAS) AF: 0.251 AC: 1300 AN: 5182

South Asian (SAS) AF: 0.641 AC: 3081 AN: 4806

European-Finnish (FIN) AF: 0.653 AC: 6869 AN: 10524

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.767 AC: 52124 AN: 67982

Other (OTH) AF: 0.805 AC: 1700 AN: 2112

Alfa AF: 0.756 Hom.: 18854

Bravo AF: 0.810

Asia WGS AF: 0.498 AC: 1734 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.018
DANN	Benign	0.39
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs7792872; hg19: chr7-106197812;