ENST00000439694.6:n.655+7139A>G

Variant names:

• chr7-137024766-T-C
• rs17506824
• ENST00000439694.6:n.655+7139A>G

Variant summary

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

The ENST00000439694.6(ENSG00000234352):​n.655+7139A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 151,836 control chromosomes in the GnomAD database, including 26,475 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 0.57 (26475 hom., cov: 32)
• Consequence: ENSG00000234352 ENST00000439694.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.883
• Publications: 1 publications found

Genes affected

ENSG00000234352 (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 (AFR) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC349160	NR_046103.1	n.341+8028A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234352	ENST00000439694.6	n.655+7139A>G		intron_variant	Intron 3 of 3	1
ENSG00000234352	ENST00000425981.2	n.341+8028A>G		intron_variant	Intron 2 of 3	2
ENSG00000234352	ENST00000586239.5	n.273+8028A>G		intron_variant	Intron 2 of 4	5

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87211 AN: 151718 Hom.: 26443 Cov.: 32

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.575 AC: 87281 AN: 151836 Hom.: 26475 Cov.: 32 AF XY: 0.568 AC XY: 42167 AN XY: 74178

African (AFR) AF: 0.701 AC: 29039 AN: 41448

American (AMR) AF: 0.447 AC: 6797 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2085 AN: 3470

East Asian (EAS) AF: 0.103 AC: 526 AN: 5118

South Asian (SAS) AF: 0.266 AC: 1281 AN: 4808

European-Finnish (FIN) AF: 0.630 AC: 6652 AN: 10554

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.574 AC: 38978 AN: 67904

Other (OTH) AF: 0.571 AC: 1208 AN: 2114

Alfa AF: 0.561 Hom.: 13894

Bravo AF: 0.570

Asia WGS AF: 0.248 AC: 864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.26
DANN	Benign	0.42
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs17506824; hg19: chr7-136709513;