6-15990685-C-T

Variant names:

• chr6-15990685-C-T
• rs1544214
• ENST00000806821.1:n.449-43246C>T

Variant summary

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

The ENST00000806821.1(ENSG00000289953):​n.449-43246C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 151,926 control chromosomes in the GnomAD database, including 11,972 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 0.39 (11972 hom., cov: 32)
• Consequence: ENSG00000289953 ENST00000806821.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.259
• Publications: 2 publications found

Genes affected

ENSG00000289953 (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 (EAS) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289953	ENST00000806821.1	n.449-43246C>T		intron_variant	Intron 2 of 3
ENSG00000289953	ENST00000806822.1	n.463-43246C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.395 AC: 59959 AN: 151808 Hom.: 11970 Cov.: 32

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.395 AC: 59981 AN: 151926 Hom.: 11972 Cov.: 32 AF XY: 0.388 AC XY: 28815 AN XY: 74228

African (AFR) AF: 0.397 AC: 16455 AN: 41400

American (AMR) AF: 0.399 AC: 6097 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1461 AN: 3470

East Asian (EAS) AF: 0.478 AC: 2468 AN: 5166

South Asian (SAS) AF: 0.370 AC: 1778 AN: 4806

European-Finnish (FIN) AF: 0.309 AC: 3253 AN: 10520

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27208 AN: 67974

Other (OTH) AF: 0.413 AC: 869 AN: 2106

Alfa AF: 0.400 Hom.: 38310

Bravo AF: 0.408

Asia WGS AF: 0.426 AC: 1481 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.65
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs1544214; hg19: chr6-15990916;