rs9310223

Variant names:

• chr3-71847228-C-A
• rs9310223
• ENST00000767728.1:n.422-5874C>A

Variant summary

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

The ENST00000767728.1(ENSG00000299970):​n.422-5874C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.831 in 152,194 control chromosomes in the GnomAD database, including 52,968 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 0.83 (52968 hom., cov: 32)
• Consequence: ENSG00000299970 ENST00000767728.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484
• Publications: 1 publications found

Genes affected

ENSG00000299970 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.874 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
ENSG00000299970	ENST00000767728.1	n.422-5874C>A		intron_variant	Intron 3 of 3
ENSG00000299970	ENST00000767729.1	n.294-4795C>A		intron_variant	Intron 3 of 3
ENSG00000299970	ENST00000767730.1	n.196-4795C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.831 AC: 126355 AN: 152076 Hom.: 52930 Cov.: 32

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.918

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.897

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.879

Gnomad OTH AF: 0.827

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

GnomAD4 genome AF: 0.831 AC: 126442 AN: 152194 Hom.: 52968 Cov.: 32 AF XY: 0.825 AC XY: 61374 AN XY: 74402

African (AFR) AF: 0.812 AC: 33722 AN: 41516

American (AMR) AF: 0.677 AC: 10342 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.799 AC: 2773 AN: 3472

East Asian (EAS) AF: 0.737 AC: 3818 AN: 5180

South Asian (SAS) AF: 0.756 AC: 3649 AN: 4826

European-Finnish (FIN) AF: 0.897 AC: 9509 AN: 10604

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.879 AC: 59805 AN: 68002

Other (OTH) AF: 0.828 AC: 1745 AN: 2108

Alfa AF: 0.842 Hom.: 34978

Bravo AF: 0.814

Asia WGS AF: 0.791 AC: 2753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.23
DANN	Benign	0.26
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs9310223; hg19: chr3-71896379;