ENST00000783087.1:n.278-1118T>C

Variant names:

• chr9-6409874-A-G
• rs7857628
• ENST00000783087.1:n.278-1118T>C

Variant summary

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

The ENST00000783087.1(ENSG00000301961):​n.278-1118T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 152,028 control chromosomes in the GnomAD database, including 9,541 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 0.35 (9541 hom., cov: 32)
• Consequence: ENSG00000301961 ENST00000783087.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 7 publications found

Genes affected

ENSG00000301961 (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 = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301961	ENST00000783087.1	n.278-1118T>C		intron_variant	Intron 1 of 1
ENSG00000301961	ENST00000783088.1	n.215-1118T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52930 AN: 151910 Hom.: 9538 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.348 AC: 52945 AN: 152028 Hom.: 9541 Cov.: 32 AF XY: 0.352 AC XY: 26185 AN XY: 74304

African (AFR) AF: 0.267 AC: 11092 AN: 41478

American (AMR) AF: 0.375 AC: 5735 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1389 AN: 3462

East Asian (EAS) AF: 0.278 AC: 1439 AN: 5178

South Asian (SAS) AF: 0.346 AC: 1665 AN: 4814

European-Finnish (FIN) AF: 0.422 AC: 4448 AN: 10544

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25898 AN: 67960

Other (OTH) AF: 0.365 AC: 770 AN: 2110

Alfa AF: 0.373 Hom.: 8828

Bravo AF: 0.340

Asia WGS AF: 0.269 AC: 937 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	0.52
DANN	Benign	0.58
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs7857628; hg19: chr9-6409874;