11-128663017-T-G

Variant names:

• chr11-128663017-T-G
• rs608871
• ENST00000572256.1:n.340+1963A>C

Variant summary

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

The ENST00000572256.1(ENSG00000245008):​n.340+1963A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.875 in 152,048 control chromosomes in the GnomAD database, including 58,401 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 0.87 (58401 hom., cov: 30)
• Consequence: ENSG00000245008 ENST00000572256.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.121

Genes affected

ENSG00000245008 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.927 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
ENSG00000245008	ENST00000572256.1	n.340+1963A>C		intron_variant	Intron 2 of 3	4
ENSG00000245008	ENST00000647054.1	n.515+1963A>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.875 AC: 132882 AN: 151930 Hom.: 58350 Cov.: 30

Gnomad AFR AF: 0.935

Gnomad AMI AF: 0.973

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.871

Gnomad EAS AF: 0.877

Gnomad SAS AF: 0.806

Gnomad FIN AF: 0.865

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.862

Gnomad OTH AF: 0.860

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

GnomAD4 genome AF: 0.875 AC: 132989 AN: 152048 Hom.: 58401 Cov.: 30 AF XY: 0.873 AC XY: 64877 AN XY: 74324

Gnomad4 AFR AF: 0.935

Gnomad4 AMR AF: 0.792

Gnomad4 ASJ AF: 0.871

Gnomad4 EAS AF: 0.877

Gnomad4 SAS AF: 0.805

Gnomad4 FIN AF: 0.865

Gnomad4 NFE AF: 0.862

Gnomad4 OTH AF: 0.862

Alfa AF: 0.864 Hom.: 51332

Bravo AF: 0.871

Asia WGS AF: 0.866 AC: 3013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.8
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs608871; hg19: chr11-128532912;