6-84779898-C-T

Variant names:

• chr6-84779898-C-T
• rs215935
• ENST00000826533.1:n.326+4601C>T

Variant summary

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

The ENST00000826533.1(ENSG00000307486):​n.326+4601C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 151,980 control chromosomes in the GnomAD database, including 14,097 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 0.40 (14097 hom., cov: 31)
• Consequence: ENSG00000307486 ENST00000826533.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.313
• Publications: 2 publications found

Genes affected

ENSG00000307486 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000826533.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307486	ENST00000826533.1		n.326+4601C>T		intron	N/A
	ENSG00000307486	ENST00000826534.1		n.359+4601C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60423 AN: 151860 Hom.: 14095 Cov.: 31

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.719

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.398 AC: 60446 AN: 151980 Hom.: 14097 Cov.: 31 AF XY: 0.403 AC XY: 29947 AN XY: 74272

African (AFR) AF: 0.146 AC: 6050 AN: 41486

American (AMR) AF: 0.396 AC: 6041 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1999 AN: 3470

East Asian (EAS) AF: 0.481 AC: 2483 AN: 5160

South Asian (SAS) AF: 0.721 AC: 3469 AN: 4810

European-Finnish (FIN) AF: 0.497 AC: 5237 AN: 10546

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33767 AN: 67926

Other (OTH) AF: 0.416 AC: 877 AN: 2110

Alfa AF: 0.450 Hom.: 4134

Bravo AF: 0.375

Asia WGS AF: 0.541 AC: 1880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.15
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs215935; hg19: chr6-85489616;