rs325648

Variant names:

• chr11-6183086-C-A
• rs325648
• ENST00000529961.1:n.286+2205G>T

Variant summary

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

The ENST00000529961.1(ENSG00000254444):​n.286+2205G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 151,988 control chromosomes in the GnomAD database, including 33,978 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 (33978 hom., cov: 32)
• Consequence: ENSG00000254444 ENST00000529961.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

Genes affected

ENSG00000254444 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.747 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
ENSG00000254444	ENST00000529961.1	n.286+2205G>T		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.657 AC: 99829 AN: 151870 Hom.: 33961 Cov.: 32

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.767

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.657 AC: 99887 AN: 151988 Hom.: 33978 Cov.: 32 AF XY: 0.655 AC XY: 48670 AN XY: 74272

Gnomad4 AFR AF: 0.478

Gnomad4 AMR AF: 0.669

Gnomad4 ASJ AF: 0.765

Gnomad4 EAS AF: 0.605

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.767

Gnomad4 NFE AF: 0.752

Gnomad4 OTH AF: 0.675

Alfa AF: 0.732 Hom.: 53309

Bravo AF: 0.645

Asia WGS AF: 0.556 AC: 1935 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.26
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs325648; hg19: chr11-6204316;