7-9788878-C-T

Variant names:

• chr7-9788878-C-T
• rs12667020
• ENST00000731005.1:n.279-28815G>A

Variant summary

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

The ENST00000731005.1(ENSG00000295572):​n.279-28815G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 151,748 control chromosomes in the GnomAD database, including 25,579 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 0.58 (25579 hom., cov: 30)
• Consequence: ENSG00000295572 ENST00000731005.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 1 publications found

Genes affected

ENSG00000295572 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375147	XR_927026.2	n.210-28815G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295572	ENST00000731005.1	n.279-28815G>A		intron_variant	Intron 2 of 3
ENSG00000295572	ENST00000731006.1	n.281+4569G>A		intron_variant	Intron 3 of 4
ENSG00000295572	ENST00000731007.1	n.242-28815G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87538 AN: 151630 Hom.: 25571 Cov.: 30

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.577 AC: 87584 AN: 151748 Hom.: 25579 Cov.: 30 AF XY: 0.576 AC XY: 42714 AN XY: 74162

African (AFR) AF: 0.630 AC: 26073 AN: 41374

American (AMR) AF: 0.481 AC: 7340 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1810 AN: 3468

East Asian (EAS) AF: 0.521 AC: 2657 AN: 5104

South Asian (SAS) AF: 0.648 AC: 3118 AN: 4810

European-Finnish (FIN) AF: 0.589 AC: 6205 AN: 10530

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38639 AN: 67908

Other (OTH) AF: 0.542 AC: 1141 AN: 2106

Alfa AF: 0.568 Hom.: 21318

Bravo AF: 0.568

Asia WGS AF: 0.587 AC: 2042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.37
DANN	Benign	0.071
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs12667020; hg19: chr7-9828507;