rs9328053

Variant names:

• chr6-1444060-T-C
• rs9328053
• ENST00000808970.1:n.226-25050A>G

Variant summary

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

The ENST00000808970.1(ENSG00000272279):​n.226-25050A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 152,142 control chromosomes in the GnomAD database, including 13,353 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 0.42 (13353 hom., cov: 33)
• Consequence: ENSG00000272279 ENST00000808970.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.290
• Publications: 2 publications found

Genes affected

ENSG00000272279 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) 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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000272279	ENST00000808970.1	n.226-25050A>G		intron_variant	Intron 2 of 2
ENSG00000272279	ENST00000808971.1	n.181-19297A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63168 AN: 152024 Hom.: 13337 Cov.: 33

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.416 AC: 63221 AN: 152142 Hom.: 13353 Cov.: 33 AF XY: 0.417 AC XY: 31025 AN XY: 74368

African (AFR) AF: 0.463 AC: 19237 AN: 41504

American (AMR) AF: 0.335 AC: 5125 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1526 AN: 3468

East Asian (EAS) AF: 0.381 AC: 1976 AN: 5184

South Asian (SAS) AF: 0.409 AC: 1973 AN: 4826

European-Finnish (FIN) AF: 0.451 AC: 4763 AN: 10558

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 27084 AN: 68000

Other (OTH) AF: 0.439 AC: 929 AN: 2114

Alfa AF: 0.400 Hom.: 6846

Bravo AF: 0.409

Asia WGS AF: 0.396 AC: 1377 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.8
DANN	Benign	0.53
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs9328053; hg19: chr6-1444295;