rs9314614

Variant names:

• chr8-6840209-C-G
• rs9314614
• ENST00000500823.4:n.360-1459C>G

Your query was ambiguous. Multiple possible variants found:

• chr8-6840209-C-G
• chr8-6840209-C-T

Variant summary

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

The ENST00000500823.4(GS1-24F4.2):​n.360-1459C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.609 in 152,032 control chromosomes in the GnomAD database, including 29,393 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 0.61 (29393 hom., cov: 33)
• Consequence: GS1-24F4.2 ENST00000500823.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.90
• Publications: 14 publications found

Genes affected

GS1-24F4.2 (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 = 0.785 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GS1-24F4.2	NR_045217.1	n.321-1459C>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GS1-24F4.2	ENST00000500823.4	n.360-1459C>G		intron_variant	Intron 2 of 2	1
GS1-24F4.2	ENST00000531701.2	n.134-1459C>G		intron_variant	Intron 2 of 4	3
GS1-24F4.2	ENST00000655804.2	n.339+3988C>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.609 AC: 92530 AN: 151914 Hom.: 29352 Cov.: 33

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.609 AC: 92624 AN: 152032 Hom.: 29393 Cov.: 33 AF XY: 0.609 AC XY: 45233 AN XY: 74310

African (AFR) AF: 0.793 AC: 32880 AN: 41484

American (AMR) AF: 0.586 AC: 8954 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1805 AN: 3468

East Asian (EAS) AF: 0.640 AC: 3320 AN: 5186

South Asian (SAS) AF: 0.669 AC: 3221 AN: 4812

European-Finnish (FIN) AF: 0.487 AC: 5130 AN: 10540

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35315 AN: 67954

Other (OTH) AF: 0.611 AC: 1289 AN: 2108

Alfa AF: 0.553 Hom.: 2980

Bravo AF: 0.624

Asia WGS AF: 0.631 AC: 2193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.31
DANN	Benign	0.36
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs9314614; hg19: chr8-6697731;