7-106769006-G-A

Variant names:

• chr7-106769006-G-A
• rs17398575
• ENST00000592441.1:n.56+1146C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000592441.1(ENSG00000243797):​n.56+1146C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 152,116 control chromosomes in the GnomAD database, including 3,644 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 0.20 (3644 hom., cov: 32)
• Consequence: ENSG00000243797 ENST00000592441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210
• Publications: 38 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.309 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000243797	ENST00000592441.1	TSL:2	n.56+1146C>T		intron	N/A
	ENSG00000243797	ENST00000789608.1		n.110-3730C>T		intron	N/A
	ENSG00000243797	ENST00000789610.1		n.109+1146C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30791 AN: 151998 Hom.: 3644 Cov.: 32

Gnomad AFR AF: 0.0820

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.202 AC: 30794 AN: 152116 Hom.: 3644 Cov.: 32 AF XY: 0.208 AC XY: 15443 AN XY: 74352

African (AFR) AF: 0.0820 AC: 3404 AN: 41518

American (AMR) AF: 0.187 AC: 2854 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 845 AN: 3470

East Asian (EAS) AF: 0.135 AC: 698 AN: 5174

South Asian (SAS) AF: 0.322 AC: 1556 AN: 4826

European-Finnish (FIN) AF: 0.341 AC: 3600 AN: 10558

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16964 AN: 67994

Other (OTH) AF: 0.223 AC: 471 AN: 2112

Alfa AF: 0.224 Hom.: 9474

Bravo AF: 0.181

Asia WGS AF: 0.231 AC: 801 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.41
PhyloP100		0.021

Splicing

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

Other links and lift over

dbSNP: rs17398575; hg19: chr7-106409452;