rs717796

chr6-127468834-G-A

Variant summary

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

The NR_174482.1(SOGA3-KIAA0408):n.3890+4246C>T 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 0.663 in 152,060 control chromosomes in the GnomAD database, including 33,664 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 0.66 (33664 hom., cov: 33)
• Consequence: SOGA3-KIAA0408 NR_174482.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.888

Genes affected

SOGA3-KIAA0408 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SOGA3-KIAA0408	NR_174482.1	n.3890+4246C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.663 AC: 100746 AN: 151942 Hom.: 33622 Cov.: 33

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.663 AC: 100847 AN: 152060 Hom.: 33664 Cov.: 33 AF XY: 0.659 AC XY: 48995 AN XY: 74328

Gnomad4 AFR AF: 0.730

Gnomad4 AMR AF: 0.686

Gnomad4 ASJ AF: 0.606

Gnomad4 EAS AF: 0.717

Gnomad4 SAS AF: 0.539

Gnomad4 FIN AF: 0.605

Gnomad4 NFE AF: 0.636

Gnomad4 OTH AF: 0.647

Alfa AF: 0.646 Hom.: 6464

Bravo AF: 0.675

Asia WGS AF: 0.608 AC: 2115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.18
Dann	Benign	0.69

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs717796; hg19: chr6-127789979; COSMIC: COSV64105736;