rs17398575

chr7-106769006-G-A

Variant summary

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

The ENST00000592441.1(ENSG00000243797):n.56+1146C>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 0.202 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: ENST00000592441.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210

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 (SAS) allele frequency at 95% confidence interval = 0.309 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.56+1146C>T		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.0820

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.223

Alfa AF: 0.236 Hom.: 2662

Bravo AF: 0.181

Asia WGS AF: 0.231 AC: 801 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	2.0
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17398575; hg19: chr7-106409452;