rs717796

Variant names:

• chr6-127468834-G-A
• rs717796
• ENST00000481848.6:n.*201+4246C>T

Variant summary

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

The ENST00000481848.6(ENSG00000255330):​n.*201+4246C>T variant causes a intron 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: ENSG00000255330 ENST00000481848.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.888
• Publications: 4 publications found

Genes affected

ENSG00000255330 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SOGA3-KIAA0408	NR_174482.1	n.3890+4246C>T		intron_variant	Intron 7 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000255330	ENST00000481848.6	n.*201+4246C>T		intron_variant	Intron 7 of 11	5		ENSP00000455908.1
ENSG00000255330	ENST00000464495.4	n.*201+4246C>T		intron_variant	Intron 2 of 3	5		ENSP00000456668.2
ENSG00000255330	ENST00000473298.6	n.*201+4246C>T		intron_variant	Intron 2 of 6	2		ENSP00000456172.1
ENSG00000255330	ENST00000474293.2	n.540+4246C>T		intron_variant	Intron 2 of 2	3

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

African (AFR) AF: 0.730 AC: 30276 AN: 41476

American (AMR) AF: 0.686 AC: 10499 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2104 AN: 3472

East Asian (EAS) AF: 0.717 AC: 3701 AN: 5160

South Asian (SAS) AF: 0.539 AC: 2594 AN: 4816

European-Finnish (FIN) AF: 0.605 AC: 6383 AN: 10552

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.636 AC: 43235 AN: 67974

Other (OTH) AF: 0.647 AC: 1367 AN: 2112

Alfa AF: 0.646 Hom.: 10899

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
PhyloP100		-0.89

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

Other links and lift over

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