rs9312652

Variant names:

• chr4-54792025-G-A
• rs9312652
• ENST00000821119.1:n.609+7184G>A

Variant summary

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

The ENST00000821119.1(ENSG00000306785):​n.609+7184G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0645 in 152,186 control chromosomes in the GnomAD database, including 901 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 0.065 (901 hom., cov: 32)
• Consequence: ENSG00000306785 ENST00000821119.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 1 publications found

Genes affected

ENSG00000306785 (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 (AFR) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377657	XR_941055.3	n.360+16337G>A		intron_variant	Intron 2 of 2
LOC105377657	XR_941057.3	n.271+16426G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306785	ENST00000821119.1	n.609+7184G>A		intron_variant	Intron 3 of 3
ENSG00000306785	ENST00000821120.1	n.847+7184G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.0645 AC: 9801 AN: 152068 Hom.: 899 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0341

Gnomad ASJ AF: 0.000577

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0237

Gnomad FIN AF: 0.00339

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.00979

Gnomad OTH AF: 0.0483

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

GnomAD4 genome AF: 0.0645 AC: 9822 AN: 152186 Hom.: 901 Cov.: 32 AF XY: 0.0621 AC XY: 4624 AN XY: 74410

African (AFR) AF: 0.202 AC: 8374 AN: 41504

American (AMR) AF: 0.0340 AC: 520 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.000577 AC: 2 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5170

South Asian (SAS) AF: 0.0235 AC: 113 AN: 4816

European-Finnish (FIN) AF: 0.00339 AC: 36 AN: 10620

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.00979 AC: 666 AN: 68002

Other (OTH) AF: 0.0478 AC: 101 AN: 2114

Alfa AF: 0.0316 Hom.: 183

Bravo AF: 0.0721

Asia WGS AF: 0.0260 AC: 91 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	0.0040
DANN	Benign	0.45
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs9312652; hg19: chr4-55658191;