rs823968

Variant names:

• chr3-135341215-C-T
• rs823968
• ENST00000649588.1:n.108-80156G>A

Variant summary

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

The ENST00000649588.1(ENSG00000240086):​n.108-80156G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.74 in 151,966 control chromosomes in the GnomAD database, including 42,120 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 0.74 (42120 hom., cov: 31)
• Consequence: ENSG00000240086 ENST00000649588.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.683
• Publications: 3 publications found

Genes affected

ENSG00000240086 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.853 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
ENSG00000240086	ENST00000649588.1	n.108-80156G>A		intron_variant	Intron 1 of 6
ENSG00000240086	ENST00000655873.1	n.366+38047G>A		intron_variant	Intron 3 of 3
ENSG00000240086	ENST00000815171.1	n.122-80156G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.740 AC: 112420 AN: 151848 Hom.: 42070 Cov.: 31

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.799

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.740 AC: 112522 AN: 151966 Hom.: 42120 Cov.: 31 AF XY: 0.734 AC XY: 54537 AN XY: 74276

African (AFR) AF: 0.860 AC: 35675 AN: 41460

American (AMR) AF: 0.742 AC: 11332 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.825 AC: 2859 AN: 3464

East Asian (EAS) AF: 0.695 AC: 3591 AN: 5164

South Asian (SAS) AF: 0.633 AC: 3056 AN: 4828

European-Finnish (FIN) AF: 0.606 AC: 6384 AN: 10534

Middle Eastern (MID) AF: 0.805 AC: 235 AN: 292

European-Non Finnish (NFE) AF: 0.694 AC: 47124 AN: 67934

Other (OTH) AF: 0.743 AC: 1569 AN: 2112

Alfa AF: 0.705 Hom.: 19502

Bravo AF: 0.759

Asia WGS AF: 0.674 AC: 2343 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.65
DANN	Benign	0.24
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs823968; hg19: chr3-135060057;