17-6238357-A-C

Variant names:

• chr17-6238357-A-C
• rs7503953
• ENST00000761409.1:n.152+237T>G

Variant summary

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

The ENST00000761409.1(ENSG00000299170):​n.152+237T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.805 in 152,044 control chromosomes in the GnomAD database, including 49,382 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 0.80 (49382 hom., cov: 33)
• Consequence: ENSG00000299170 ENST00000761409.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165
• Publications: 12 publications found

Genes affected

ENSG00000299170 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.83 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000761409.1. 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
	ENSG00000299170	ENST00000761409.1		n.152+237T>G		intron	N/A
	ENSG00000299154	ENST00000761288.1		n.-126A>C		upstream_gene	N/A
	ENSG00000299154	ENST00000761289.1		n.-72A>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.805 AC: 122262 AN: 151926 Hom.: 49343 Cov.: 33

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.934

Gnomad AMR AF: 0.789

Gnomad ASJ AF: 0.838

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.904

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.830

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

GnomAD4 genome AF: 0.805 AC: 122355 AN: 152044 Hom.: 49382 Cov.: 33 AF XY: 0.801 AC XY: 59507 AN XY: 74308

African (AFR) AF: 0.781 AC: 32404 AN: 41478

American (AMR) AF: 0.788 AC: 12034 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.838 AC: 2905 AN: 3466

East Asian (EAS) AF: 0.737 AC: 3782 AN: 5134

South Asian (SAS) AF: 0.690 AC: 3325 AN: 4822

European-Finnish (FIN) AF: 0.777 AC: 8203 AN: 10552

Middle Eastern (MID) AF: 0.890 AC: 260 AN: 292

European-Non Finnish (NFE) AF: 0.836 AC: 56844 AN: 68016

Other (OTH) AF: 0.828 AC: 1748 AN: 2110

Alfa AF: 0.823 Hom.: 30757

Bravo AF: 0.807

Asia WGS AF: 0.736 AC: 2559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.5
DANN	Benign	0.73
PhyloP100		0.17

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: rs7503953;

hg19: chr17-6141677;