chr7-150779800-G-A

Variant names:

• chr7-150779800-G-A
• rs7806458
• ENST00000692358.2:n.487-715C>T

Variant summary

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

The ENST00000692358.2(ENSG00000289470):​n.487-715C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.706 in 151,648 control chromosomes in the GnomAD database, including 38,725 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 0.71 (38725 hom., cov: 29)
• Consequence: ENSG00000289470 ENST00000692358.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570
• Publications: 34 publications found

Genes affected

ENSG00000289470 (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 (AFR) allele frequency at 95% confidence interval = 0.86 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000692358.2. 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
	ENSG00000289470	ENST00000692358.2		n.487-715C>T		intron	N/A
	ENSG00000289470	ENST00000745634.1		n.447+883C>T		intron	N/A
	ENSG00000289470	ENST00000745635.1		n.416+883C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.706 AC: 106964 AN: 151534 Hom.: 38687 Cov.: 29

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.706 AC: 107060 AN: 151648 Hom.: 38725 Cov.: 29 AF XY: 0.701 AC XY: 51900 AN XY: 74052

African (AFR) AF: 0.868 AC: 35913 AN: 41392

American (AMR) AF: 0.695 AC: 10588 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.740 AC: 2565 AN: 3466

East Asian (EAS) AF: 0.623 AC: 3209 AN: 5148

South Asian (SAS) AF: 0.690 AC: 3322 AN: 4812

European-Finnish (FIN) AF: 0.558 AC: 5813 AN: 10422

Middle Eastern (MID) AF: 0.685 AC: 200 AN: 292

European-Non Finnish (NFE) AF: 0.639 AC: 43408 AN: 67880

Other (OTH) AF: 0.726 AC: 1528 AN: 2104

Alfa AF: 0.657 Hom.: 122262

Bravo AF: 0.721

Asia WGS AF: 0.675 AC: 2350 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	6.1
DANN	Benign	0.46
PhyloP100		0.057

Splicing

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

Other links and lift over

dbSNP: rs7806458; hg19: chr7-150476888;