rs17315854

Variant names:

• chr7-86024657-T-C
• rs17315854
• ENST00000757672.1:n.224-58056A>G

Variant summary

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

The ENST00000757672.1(ENSG00000298738):​n.224-58056A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0961 in 151,940 control chromosomes in the GnomAD database, including 805 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 0.096 (805 hom., cov: 32)
• Consequence: ENSG00000298738 ENST00000757672.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.987
• Publications: 2 publications found

Genes affected

ENSG00000298738 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000757672.1. 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
	ENSG00000298738	ENST00000757672.1		n.224-58056A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0961 AC: 14593 AN: 151822 Hom.: 804 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.0447

Gnomad ASJ AF: 0.0680

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.0242

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0732

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

GnomAD4 genome AF: 0.0961 AC: 14604 AN: 151940 Hom.: 805 Cov.: 32 AF XY: 0.0952 AC XY: 7069 AN XY: 74276

African (AFR) AF: 0.112 AC: 4661 AN: 41502

American (AMR) AF: 0.0446 AC: 679 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.0680 AC: 236 AN: 3472

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5152

South Asian (SAS) AF: 0.0244 AC: 118 AN: 4830

European-Finnish (FIN) AF: 0.147 AC: 1562 AN: 10592

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7084 AN: 67850

Other (OTH) AF: 0.0724 AC: 153 AN: 2112

Alfa AF: 0.0949 Hom.: 1258

Bravo AF: 0.0892

Asia WGS AF: 0.0170 AC: 60 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.0
DANN	Benign	0.67
PhyloP100		-0.99

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17315854;

hg19: chr7-85653973;