rs9314614

chr8-6840209-C-Gchr8-6840209-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_045217.1(GS1-24F4.2):n.321-1459C>G variant causes a intron, non coding transcript 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 NR_045217.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.90

Genes affected

GS1-24F4.2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
GS1-24F4.2	NR_045217.1	n.321-1459C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GS1-24F4.2	ENST00000500823.3	n.340-1459C>G		intron_variant, non_coding_transcript_variant		1
GS1-24F4.2	ENST00000655804.1	n.322+3988C>G		intron_variant, non_coding_transcript_variant
GS1-24F4.2	ENST00000657010.1	n.323-1459C>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.793

Gnomad4 AMR AF: 0.586

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.640

Gnomad4 SAS AF: 0.669

Gnomad4 FIN AF: 0.487

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.611

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9314614; hg19: chr8-6697731;