ENST00000778316.1:n.385-28836T>A

Variant names:

• chr9-21307785-T-A
• rs3758236
• ENST00000778316.1:n.385-28836T>A

Variant summary

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

The ENST00000778316.1(ENSG00000301340):​n.385-28836T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,034 control chromosomes in the GnomAD database, including 3,956 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 0.22 (3956 hom., cov: 32)
• Consequence: ENSG00000301340 ENST00000778316.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.132
• Publications: 6 publications found

Genes affected

ENSG00000301340 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987053	XR_001746634.2	n.472-28836T>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301340	ENST00000778316.1	n.385-28836T>A		intron_variant	Intron 2 of 2
ENSG00000301340	ENST00000778317.1	n.539-28836T>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32796 AN: 151916 Hom.: 3951 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.216 AC: 32842 AN: 152034 Hom.: 3956 Cov.: 32 AF XY: 0.218 AC XY: 16198 AN XY: 74324

African (AFR) AF: 0.259 AC: 10724 AN: 41474

American (AMR) AF: 0.269 AC: 4102 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 695 AN: 3462

East Asian (EAS) AF: 0.474 AC: 2445 AN: 5162

South Asian (SAS) AF: 0.152 AC: 733 AN: 4812

European-Finnish (FIN) AF: 0.194 AC: 2050 AN: 10570

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11475 AN: 67962

Other (OTH) AF: 0.207 AC: 437 AN: 2110

Alfa AF: 0.200 Hom.: 390

Bravo AF: 0.226

Asia WGS AF: 0.299 AC: 1038 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.41
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs3758236; hg19: chr9-21307784;