rs912056

Variant names:

• chr6-6735964-A-T
• rs912056
• ENST00000648205.2:n.122+2945T>A

Variant summary

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

The ENST00000648205.2(ENSG00000226281):​n.122+2945T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 152,006 control chromosomes in the GnomAD database, including 33,279 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 0.65 (33279 hom., cov: 31)
• Consequence: ENSG00000226281 ENST00000648205.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 12 publications found

Genes affected

ENSG00000226281 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928004	NR_187687.1	n.486-24106T>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226281	ENST00000648205.2	n.122+2945T>A		intron_variant	Intron 1 of 3
ENSG00000226281	ENST00000656346.2	n.119+2945T>A		intron_variant	Intron 1 of 3
ENSG00000226281	ENST00000669831.2	n.189+2945T>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.648 AC: 98440 AN: 151888 Hom.: 33245 Cov.: 31

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.648 AC: 98509 AN: 152006 Hom.: 33279 Cov.: 31 AF XY: 0.638 AC XY: 47358 AN XY: 74284

African (AFR) AF: 0.815 AC: 33806 AN: 41482

American (AMR) AF: 0.528 AC: 8071 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 2170 AN: 3466

East Asian (EAS) AF: 0.236 AC: 1217 AN: 5162

South Asian (SAS) AF: 0.410 AC: 1975 AN: 4812

European-Finnish (FIN) AF: 0.636 AC: 6704 AN: 10548

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.627 AC: 42577 AN: 67948

Other (OTH) AF: 0.604 AC: 1270 AN: 2104

Alfa AF: 0.646 Hom.: 4027

Bravo AF: 0.646

Asia WGS AF: 0.332 AC: 1156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.037
DANN	Benign	0.70
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs912056; hg19: chr6-6736197;