rs9378283

Variant names:

• chr6-1221343-A-G
• rs9378283
• ENST00000700915.2:n.230+7048T>C

Variant summary

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

The ENST00000700915.2(ENSG00000289842):​n.230+7048T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 152,136 control chromosomes in the GnomAD database, including 6,874 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 0.29 (6874 hom., cov: 33)
• Consequence: ENSG00000289842 ENST00000700915.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.547
• Publications: 2 publications found

Genes affected

ENSG00000289842 (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 = 0.578 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
ENSG00000289842	ENST00000700915.2	n.230+7048T>C		intron_variant	Intron 1 of 2
ENSG00000289842	ENST00000702015.1	n.218+7048T>C		intron_variant	Intron 1 of 2
ENSG00000289842	ENST00000837382.1	n.111+7233T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44453 AN: 152018 Hom.: 6876 Cov.: 33

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.292 AC: 44460 AN: 152136 Hom.: 6874 Cov.: 33 AF XY: 0.292 AC XY: 21734 AN XY: 74366

African (AFR) AF: 0.259 AC: 10748 AN: 41528

American (AMR) AF: 0.207 AC: 3158 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 945 AN: 3468

East Asian (EAS) AF: 0.596 AC: 3085 AN: 5176

South Asian (SAS) AF: 0.363 AC: 1752 AN: 4822

European-Finnish (FIN) AF: 0.291 AC: 3079 AN: 10566

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20915 AN: 67978

Other (OTH) AF: 0.250 AC: 527 AN: 2112

Alfa AF: 0.302 Hom.: 5773

Bravo AF: 0.283

Asia WGS AF: 0.456 AC: 1585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.33
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs9378283; hg19: chr6-1221578;